GENETICS OF VIRUSES

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

COMPARING SIZES

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

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

VIRAL STRUCTURE

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

VIRAL LIFE CYCLES 1) INFECTING HOST CELL WITH VIRAL GENOME 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

SIMPLIFIED VIRAL REPRODUCTIVE CYCLE

VIDEO: SIMPLIFIED VIRUS LIFE CYCLE

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

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

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

LYTIC CYCLE OF PHAGE T4

LYTIC CYCLE VIDEO

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

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

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

REPRODUCTIVE CYCLES OF PHAGE L

LYSOGENIC CYCLE VIDEO

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

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

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

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

REPRODUCTIVE CYCLE OF AN ENVELOPED VIRUS

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

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

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

HIV-THE REPRODUCTIVE CYCLE

HIV RETROVIRUS VIDEO

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

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

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

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

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

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

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

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

BACTERIAL REPLICATION

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

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

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

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

TRANSDUCTION

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

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

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

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

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

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

INSERTION SEQUENCES, THE SIMPLEST TRANSPOSONS

INSERTION OF A TRANSPOSON AND CREATION OF DIRECT REPEATS

OPERONS: THE BASIC CONCEPT OPERON = A REGULATED CLUSTER OF ADJACENT STRUCTURAL GENES WITH RELATED FUNCTIONS COMMON IN BACTERIA AND PHAGES HAS A SINGLE PROMOTER REGION, SO AN RNA POLYMERASE WILL TRANSCRIBE ALL STRUCTURAL GENES ON AN ALL OR NONE BASIS

OPERONS THERE ARE 4 MAJOR COMPONENTS OF AN OPERON: 1) A REGULATORY GENE PRODUCES A REPRESSOR PROTEIN, A SUBSTANCE THAT CAN PREVENT GENE EXPRESSION BY BLOCKING THE ACTION OF RNA POLYMERASE 2) THE PROMOTER REGION IS A SEQUENCE OF DNA TO WHICH THE RNA POLYMERASE ATTACHES TO BEGIN TRANSCRIPTION

3) THE OPERATOR REGION CAN BLOCK THE ACTION OF THE RNA POLYMERASE IF THE REGION IS OCCUPIED BY A REPRESSOR PROTEIN 4) THE STRUCTURAL GENES CONTAIN DNA SEQUENCES THAT CODE FOR SEVERAL RELATED ENZYMES THAT DIRECT THE PRODUCTION OF SOME PARTICULAR END PRODUCT

REGULATION OF A METABOLIC PATHWAY

Trp OPERON AN OPERON IN E.COLI, TRP OPERON PRODUCES ENZYMES FOR THE SYNTHESIS OF THE AMINO ACID TRYPTOPHAN. THE REGULATORY GENE PRODUCES AN INACTIVE REPRESSOR THAT DOES NOT BIND TO THE OPERATOR. AS A RESULT, THE RNA POLYMERASE PROCEEDS TO TRANSCRIBE THE STRUCTURAL GENES NECESSARY TO PRODUCE ENZYMES THAT SYNTHESIZE TRPTOPHAN

WHEN TRYPTOPHAN IS AVAILABLE TO E WHEN TRYPTOPHAN IS AVAILABLE TO E.COLI FROM THE SURROUNDING ENVIRONMENT, THE BACTERIUM NO LONGER NEEDS TO MAKE ITS OWN TRYPTOPHAN. IN THIS CASE, RISING LEVELS OF TRPTOPHAN INDUCE SOME TRYPTOPHAN TO REACT WITH THE INACTIVE REPRESSOR AND MAKE IT ACTIVE. HERE TRPTOPHAN IS ACTING AS A COREPRESSOR. THE ACTIVE REPRESSOR NOW BINDS TO THE OPERATOR REGION, WHICH, IN TURN, PREVENTS THE TRANSCRIPTION OF THE STRUCTURAL GENES. SINCE THESE STRUCTURAL GENES STOP PRODUCING ENZYMES ONLY IN THE PRESENCE OF AN ACTIVE REPRESSOR, THEY ARE CALLED REPRESSIBLE ENZYMES

THE TRP OPERON

LAC OPERON THE LAC OPERON IN E.COLI CONTROLS THE BREAKDOWN OF LACTOSE. THE REGULATORY GENE IN THE LAC OPERON PRODUCES AN ACTIVE REPRESSOR THAT BINDS TO THE OPERATOR REGION. WHEN THE OPERATOR REGION IS OCCUPIED BY THE REPROSSOR, RNA POLYMERASE IS UNABLE TO TRANSCRIBE SEVERAL STRUCTURAL GENES THAT CODE FOR ENZYMES THAT CONTROL THE UPTAKE AND SUBSEQUENT BREAKDOWN OF LACTOSE.

WHEN LACTOSE IS AVAILABLE, SOME OF THE LACTOSE (IN A CONVERTED FORM) COMBINES WITH THE REPRESSOR TO MAKE IT INACTIVE. WHEN THE REPRESSOR IS INACTIVATED, RNA POLYMERSE IS ABLE TO TRANSCRIBE THE GENES THAT CODE FOR THE ENZYMES THAT BREAK DOWN LACTOSE. SINCE A SUBSTRATE (LACTOSE) IS REQUIRED TO INDUCE (TURN ON) THE OPERON, THE ENZYMES THE OPERON PRODUCES ARE SAID TO BE INDUCIBLE ENZYMES.

LAC OPERON