GENETICS OF VIRUSES

1. GENETICS OF VIRUSES

2. 1950’S- VIRUSES OBSERVED • THE SMALLEST VIRUSES ARE ONLY 20 nm IN DIAMETER • THE VIRUS PARTICLE, CONSISTS OF NUCLEIC ACID ENCLOSED BY A PROTEIN COAT • MAY BE DOUBLE-STRANDED DNA • SINGLE-STRANDED DNA • DOUBLE-STRANDED RNA • SINGLE-STRANDED RNA

3. COMPARING SIZES

4. CAPSIDS • CAPSIDS ARE THE PROTEIN COAT THAT ENCLOSES THE VIRAL GENOME • MAY BE ROD-SHAPED, POLYHEDRAL OR COMPLEX • COMPOSED OF MANY CAPSOMERES, PROTEIN SUBUNITS MADE FROM ONLY ONE OR A FEW TYPES OF PROTEINS

5. ENVELOPE • THE ENVELOPE IS THE MEMBRNE THAT COVERS SOME VIRAL CAPSIDS • IT HELPS VIRUSES INFECT THEIR HOST • IT IS DERIVED FROM HOST CELL MEMBRANE

6. VIRAL STRUCTURE

7. VIRAL REPRODUCTION OVERVIEW • VIRUSES CAN ONLY REPRODUCE INSIDE OF A HOST CELL • OBLIGATE INTRACELLULAR PARASITES-CAN EXPRESS THEIR GENES AND REPRODUCE ONLY WITHIN A LIVING CELL • HOST RANGE = LIMITED NUMBER OR RANGE OF HOST CELLS THAT A PARASITE CAN INFECT

8. VIRAL LIFE CYCLES GENERAL PATTERNS: • 1) INFECTING HOST CELL WITH VIRAL GENOME • 2) CO-OPTING HOST CELL’S RESOURCES TO: A) REPLICATE THE VIRAL GENOME B) MANUFACTURE CAPSID PROTEIN • 3) ASSEMBLING NEWLY PRODUCES VIRAL NUCLIC ACID AND CAPSOMERES INTO THE NEXT GENERATION OF VIRUSES

9. SIMPLIFIED VIRAL REPRODUCTIVE CYCLE

10. VIDEO: SIMPLIFIED VIRUS LIFE CYCLE

11. BACTERIOPHAGE • A PHAGE IS A VIRUS THAT ATTACKS BACTERIA • PHAGES ARE THE BEST UNDERSTOOD OF ALL VIRUSES

12. THE LYTIC CYCLE • VIRULENT BACTERIOPHAGES REPRODUCE ONLY BY A LYTIC REPLICATION CYCLE • VIRULENT PHAGES - PHAGES THAT LYSE THEIR HOST CELLS • LYTIC CYCLE = A VIRAL REPLICATION CYCLE THAT RESULTS IN DEATY (LYSIS) OF THE HOST CELL

13. STEPS OF THE LYTIC CYCLE • 1) PHAGE ATTACHES TO CELL SURFACE • 2) PHAGE CONTRACTS SHEATH AND INJECTS DNA • 3) HYDROLYTIC ENZYMES DESTROY HOST CELL’S DNA • 4) PHAGE GENOME DIRECTS HOST CELL TO PRODUCE PHAGE COMPONENTS: DNA AND CAPSID PROTEINS • 5) CELL LYSES AND RELEASES PHAGE PARTICLES

14. LYTIC CYCLE OF PHAGE T4

15. LYTIC CYCLE VIDEO

16. BACTERIAL DEFENSES • BACTERIAL MUTATIONS CAN CHANGE RECEPTOR SITES USED BY PHAGES FOR RECOGNITION, AND THUS AVOID INFECTION • BACTERIAL RESTRICTION NUCLEASES RECOGNIZE AND CUT UP FOREIGN DNA, INCLUDING CERTAIN PHAGE DNA. BACTERIAL DNA IS CHEMICALLY ALTERED, SO IT IS NOT DESTROYED BY THE CELL’S OWN RESTRICTION ENZYMES

17. LYSOGENIC CYCLE • SOME VIRUSES CAN COEXIST WITH THEIR HOSTS BY INCORPORATING THEIR GENOME INTO THE HOST’S GENOME • TEMPERATE VIRUSES - VIRUSES THAT CAN INTEGRATE THEIR GENOME INTO A HOST CHROMOSOME AND REMAIN LATENT UNTIL THEY INITIATE A LYTIC CYCLE • THEY HAVE TWO POSSIBLE MODES OF REPRODUCTION, THE LYTIC CYCLE AND THE LYSOGENIC CYCLE

18. STEPS OF LYSOGENIC CYCLE • PHAGE L LIFE CYCLE • 1) PHAGE L BINDS TO THE SURFACE OF E.COLI CELL • 2) PHAGE L INJECTS ITS DNA INTO THE BACTERIAL HOST CELL • 3) L DNA FORMS A CIRCLE AND EITHER BEGINS A LYTIC OR LYSOGENIC CYCLE • 4) L DNA INSERTS BY GENETIC RECOMBINATION (CROSSING OVER) INTO A SPECIFIC SITE ON THE BACTERIAL CHROMOSOME

19. REPRODUCTIVE CYCLES OF PHAGE L

20. LYSOGENIC CYCLE VIDEO

21. PROPHAGES • A PHAGE GENOME THAT IS INCORPORATED INTO A SPECIFIC SITE ON THE BACTERIAL CHROMOSOME

22. VIRAL ENVELOPES • SOME ANIMAL VIRUSES ARE SURROUNDED BY A MEMBRANOUS ENVELOPE, WHICH IS UNIQUE TO SEVERAL GROUPS OF ANIMAL VIRUSES. THIS ENVELOPE IS: • OUTSIDE THE CAPSID AND HELPS THE VIRUS ENTER HOST CELLS • A LIPID BILAYER WITH GLYCOPROTEIN SPIKES PROTRUDING FROM THE OUTER SURFACE

23. ENVELOPED VIRUSES LIFE CYCLE • 1) ATTACHMENT - GLYCOPROTEIN SPIKES PROTRUDING FROM THE VIRAL ENVELOPE ATTACH TO RECEPTOR SITES ON THE HOST’S PLASMA MEMBRANE • 2) ENTRY - AS THE ENVELOPE FUSES WITH THE MEMBRANE, THE ENTIRE VIRUS (CAPSID AND GENOME) IS TRANSPORTED INTO THE CYTOPLASM BY RECEPTOR-MEDIATED ENDOCYTOSIS

24. 3) UNCOATING - CELLULAR ENZYMES UNCOAT THE GENOME BY REMOVING THE PROTEIN CAPSID FROM THE VIRAL RNA • 4) VIRAL RNA AND PROTEIN SYNTHESIS-VIRAL ENZYMES ARE REQUIRED TO REPLICATE THE RNA GENOME AND TO TRANSCRIBE mRNA • 5) ASSEMBLY AND RELEASE - NEW CAPSIDS SURROUND VIRAL GENOMES. ONCE ASSEMBLED, THE VIRIONS ENVELOP WITH HOST PLASMA MEMBRANE AS THEY BUD OFF FROM THE CELL’S SURFACE

25. REPRODUCTIVE CYCLE OF AN ENVELOPED VIRUS

26. PROVIRUS • A PROVIRUS IS FORMED WHEN VIRAL DNA INSERTS INTO A HOST CELL CHROMOSOME. (IF IT IS A BACTERIA CELL, IT IS CALLED A PROPHAGE). PROVIRUS’ REMAIN DORMANT UNTIL SOME TRIGGER (USUALLY ENVIRONMENTAL) CAUSES THE VIRUS TO BEGIN THE DESTRUCTIVE LYTIC CYCLE

27. RNA VIRUSES • USE RNA TO CARRY GENETIC INFORMATION • THE REPRODUCTIVE CYCLES DEVIATE FROM THE STANDARD LYTIC AND LYSOGENIC CYCLES • IN SOME RNA VIRUSES, THE VIRAL RNA IS USED DIRECTLY AS mRNA

28. RETROVIRUSES • RETRO = BACKWARD • RETROVIRUS= RNA VIRUS THAT USES REVERSE TRANSCRIPTASE TO TRANSCRIBE DNA FROM THE VIRAL RNA GENOME • HIV-THE VIRUS THAT CAUSES AIDS IS A RETROVIRUS • RETROVIRUSES HAVE COMPLEX CYCLES BECAUSE THEY MUST FIRST CARRY OUT REVERSE TRANSCRIPTION

29. HIV-THE REPRODUCTIVE CYCLE

30. HIV RETROVIRUS VIDEO

31. VIRUSES AND CANCER • SOME TUMOR VIRUSES CAUSE CANCER IN ANIMALS • WHEN ANIMAL CELLS GROWN IN TISSUE CULTURE ARE INFECTED WITH TUMOR VIRUSES, THEY TRANSFORM TO A CANCEROUS STATE • EXAMPLES ARE MEMBERS OF THE RETROVIRUS, PAPOVAVIRUS, ADENOVIRUS, HERPESVIRUS GROUPS • CERTAIN VIRUSES ARE IMPLICATED IN HUMAN CANCERS

32. VIRUSES AND CANCER • RETROVIRUS - LEUKEMIA • HERPESVIRUS - BURKITT’S LYMPHOMA • PAPILOMA VIRUS - CERVICAL CANCER • HEPATITIS B - LIVER CANCER • ONCOGENES - GENES FOUND IN VIRUSES OR AS PART OF THE NORMAL GENOME, THAT TRIGGER TRANSFORMATION OF A CELL TO A CANCEROUS STATE

33. PLANT VIRUSES • AS SERIOUS AGRICUTURAL PESTS, MANY OF THE PLANT VIRUSES: • STUNT PLANT GROWTH AND DIMINISH CROP YIELDS • ARE RNA VIRUSES • HAVE ROD-SHAPED CAPSIDS WITH CAPSOMERES ARRANGED IN A SPIRAL CAPSOMERE - COMPLEX CAPSID SUBUNIT CONSISTING OF SEVERAL IDENTICAL OR DIFFERENT PROTEIN MOLECULES

34. PLANT VIRUSES • PLANT VIRUSES SPREAD FROM PLANT TO PLANT BY TWO MAJOR ROUTES: • 1) HORIZONTAL TRANSMISSION - AN ORGANISM RECEIVES THE VIRUS FROM AN EXTERNAL SOURCE SUCH AS INSECTS OR GARDENING TOOLS • 2) VERTICAL TRANSMISSION - AN ORGANISM INHERITS A VIRAL INFECTION FROM ITS PARENT

35. VIROIDS • ANOTHER CLASS OF PLANT PATHOGENS, ARE SMALLER AND SIMPLER THAN VIRUSES • THEY ARE SMALL, NAKED, CIRCULAR RNA MOLECULES THAT DO NOT ENCODE PROTEIN, BUT CAN REPLICATE IN HOST PLANT CELLS • THEY DISRUPT NORMAL PLANT METABOLISM, DEVELOPMENT, AND GROWTH BY CAUSING ERRORS IN GENE EXPRESSION • VIROID DISEASES AFFECT MANY COMMERCIALLY IMPORTANT PLANTS SUCH AS COCONUT PALMS, POTATOES, TOMATOES

36. PRIONS • PRIONS ARE PATHOGENS THAT ARE PROTEINS, AND THEY APPEAR TO CAUSE A NUMBER OF DEGENERATIVE BRAIN DISEASES SUCH AS: • SCAPIE IN SHEEP • MAD COW DISEASE • CREUTZFELDT-JAKOB DISEASE IN HUMANS

37. HOW PRIONS MAY PROPAGATE WHEN A PRION CONTACTS ITS NORMAL “TWIN”, IT MAY INDUCE THE NORMAL PROTEIN TO ASSUME THE ABNORMAL SHAPE. THE RESULTING CHAIN REACTION MAY CONTINUE UNTIL PRIONS ACCUMULATE TO DANGEROUS LEVELS, CAUSING CELLULAR MALFUNCTION

38. GENETICS OF BACTERIA • BACTERIA ARE PROKARYOTES • THEY DO NOT POSSESS ANY OF THE SPECIALIZED ORGANELLES OF EUKARYOTES • HAS A SINGLE, CIRCULAR DNA • REPRODUCES BY BINARY FISSION-THE CHROMOSOME REPLICATES AND THE CELL DIVIDES INTO TWO CELLS

39. BACTERIAL REPLICATION

40. PLASMIDS • BACTERIA ALSO CONTAIN PLASMIDS, SHORT, CIRCULAR DNA MOLECULES OUTSIDE THE CHROMOSOME • PLASMIDS CARRY GENES THAT ARE BENEFICIAL BUT NOT NORMALLY ESSENTIAL TO THE SURVIVAL OF THE BACTERIUM • PLASMIDS REPLICATE INDEPENDENTLY OF THE CHROMOSOME • EPISOMES = PLASMIDS THAT BECOME INCORPORATED INTO THE BACTERIAL CHROMOSOME

41. GENETIC RECOMBINATION IN BACTERIA • THERE ARE 3 NATURAL PROCESSES OF GENETIC RECOMBINATION IN BACTERIA: • TRANSFORMATION • TRANSDUCTION • CONJUGATION

42. TRANSFORMATION • THE PROCESS OF GENE TRANSFER DURING WHICH A BACTERIAL CELL ASSIMILATES FOREIGN DNA FROM THE SURROUNDINGS • ASSIMILATED FOREIGN DNA MAY BE INTEGRATED INTO THE BACTERIAL CHROMOSOME BY RECOMBINATION • PROGENY WILL CARRY A NEW COMBINATION OF GENES

43. TRANSDUCTION • GENE TRANSFER FROM ONE BACTERIUM TO ANOTHER BY A BACTERIOPHAGE • RANDOM PIECES OF HOST CELL DNA ARE PACKAGED WITHIN A PHAGE CAPSID DURING THE LYTIC CYCLE OF A PHAGE • THIS PROCESS CAN TRANSFER ALMOST ANY HOST GENE AND LITTLE OR NO PHAGE GENES • WHEN THE PHAGE PARTICLE INFECTS A NEW HOST CELL, THE DONOR CELL DNA CAN RECOMBINE WITH THE RECIPIENT CELL DNA

44. TRANSDUCTION

45. CONJUGATION • THE DIRECT TRANSFER OF GENES BETWEEN TWO CELLS THAT ARE TEMPORARILY JOINED • CYCLE: DNA-DONATING CELL EXTENDS EXTERNAL APPENDAGES CALLED SEX PILI • SEX PILI ATTACH TO A DNA-RECEIVING CELL • A CYTOPLASMIC BRIDGE FORMS THROUGH WHICH DNA TRANSFER OCCURS

46. PLASMIDS • PLASMIDS ARE SMALL, CIRCULAR, DOUBLE-STRANDED, SELF-REPLICATING MOLECULAR RINGS OF DNA THAT CARRY EXTRACHROMOSOMAL GENES IN SOME BACTERIA • PLASMIDS CARRY GENES THT ARE BENEFICIAL BUT NOT NORMALLY ESSENTIAL TO SURVIVAL OF THE BACTERIA • PLASMIDS REPLICATE INDEPENDENTLY OF THE CHROMOSOME • EPISOMES = PLASMIDS THAT BECOME INCORPORATED INTO THE BACTERIAL CHROMOSOME

47. F PLASMID • THE F PLASMID (F FOR FERTILITY) HAS ABOUT 25 GENES, MOST OF WHICH ARE INVOLVED IN THE PRODUCTION OF SEX PILI • WHEN A RECIPIENT BACTERIUM RECeiVES THE F PLASMID, IT TOO CAN BECOME A DONOR CELL

48. R PLASMID • R PLASMIDS PROVIDE BACTERIA WITH RESISTANCE AGAINST ANTIBODIES • SOME CARRY UP TO 10 GENES FOR RESISTANCE TO ANTIBODIES • R PLASMIDS CAN TRANSFER RESISTANCE GENES TO BACTERIA OF DIFFERENT SPECIES INCLUDING PATHOGENIC STRAINS. AS A CONSEQUENCE, RESISTANCE STRAINS OF PATHOGENS ARE BECOMING MORE COMMON

49. TRANSPOSONS • TRANSPOSONS ARE PIECES OF DNA, OR TRANSPOSIBLE GENETIC ELEMENTS, WHICH CAN ACTUALLY MOVE FROM ONE LOCATION TO ANOTHER IN A CELL’S GENOME • CONSERVATIVE TRANSPOSITION = MOVEMENT OF PREEXISTING GENES FROM ONE GENOMIC LOCATION TO ANOTHER; THE TRANSPOSON’S GENES ARE NOT REPLICATED BEFORE THE MOVE, SO THE NUMBER OF GENE COPIES IS CONSERVED • REPLICATIVE TRANSPOSITION = MOVEMENT OF GENE COPIES FROM THEIR ORIGINAL SITE OR REPLICATON TO ANOTHER LOCATION; THE TRANSPOSON’S GENES ARE INSERTED AT SOME NEW SITE WITHOUT BEING LOST FROM THE ORIGINAL SITE

50. INSERTION SEQUENCES • THE SIMPLEST TRANSPOSONS, WHICH CONTAIN ONLY THE GENES NECESSARY FOR THE PROCESS OF TRANSPOSITION. INSERTION SEQUENCE DNA INCLUDES TWO ESSENTIAL TYPES OF NUCLEOTIDE SEQUENCES: • 1) NUCLEOTIDE SEQUENCE CODING FOR TRANSPOSASE • 2) INVERTED REPEATS TRANSPOSASE = ENZYME THAT CATALYZES INSERTION OF TRANSPOSONS INTO NEW SITES INVERTED REPEATS (IR) = SHORT NONCODING NUCLEOTIDE SEQUENCES OF DNA THAT ARE REPEATED IN REVERSE ORDER ON OPPOSITE ENDS OF A TRANSPOSON