Q1 vs. Q2 GradesGrade 1st Quarter 2nd Quarter

A 55 75B 32 27C 21 16D 7 8F 19 5

Figure 18.6 The lytic cycle of phage T4, a virulent phage

Attachment. The T4 phage usesits tail fibers to bind to specificreceptor sites on the outer surface of an E. coli cell.

Entry of phage DNA and degradation of host DNA.The sheath of the tail contracts,injecting the phage DNA intothe cell and leaving an emptycapsid outside. The cell’sDNA is hydrolyzed.

Synthesis of viral genomes and proteins. The phage DNAdirects production of phageproteins and copies of the phagegenome by host enzymes, usingcomponents within the cell.

Assembly. Three separate sets of proteinsself-assemble to form phage heads, tails,and tail fibers. The phage genome ispackaged inside the capsid as the head forms.

Release. The phage directs productionof an enzyme that damages the bacterialcell wall, allowing fluid to enter. The cellswells and finally bursts, releasing 100 to 200 phage particles.

12

4 3

5

Phage assembly

Head Tails Tail fibers

Figure 18.7 The lytic and lysogenic cycles of phage , a temperate phage

Many cell divisions produce a large population of bacteria infected with the prophage.

The bacterium reproducesnormally, copying the prophageand transmitting it to daughter cells.

Phage DNA integrates into the bacterial chromosome,becoming a prophage.

New phage DNA and proteins are synthesized and assembled into phages.

Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle.

Certain factorsdetermine whether

The phage attaches to ahost cell and injects its DNA.

Phage DNAcircularizes

The cell lyses, releasing phages.Lytic cycleis induced

Lysogenic cycleis entered

Lysogenic cycleLytic cycle

or Prophage

Bacterialchromosome

Phage

PhageDNA

Figure 18.10 The reproductive cycle of HIV, a retrovirus

Vesicles transport theglycoproteins from the ER tothe cell’s plasma membrane.

7

The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER).

6

The double-stranded DNA is incorporatedas a provirus into the cell’s DNA.

4

Proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral proteins.

5

Reverse transcriptasecatalyzes the synthesis ofa second DNA strandcomplementary to the first.

3

Reverse transcriptasecatalyzes the synthesis of aDNA strand complementaryto the viral RNA.

2

New viruses budoff from the host cell.9

Capsids areassembled aroundviral genomes and reverse transcriptase molecules.

8

mRNA

RNA genomefor the nextviral generation

Viral RNA

RNA-DNAhybrid

DNA

ChromosomalDNA

NUCLEUSProvirus

HOST CELL

Reverse transcriptase

New HIV leaving a cell

HIV entering a cell

0.25 µm

HIV Membrane of white blood cell

The virus fuses with thecell’s plasma membrane.The capsid proteins areremoved, releasing the viral proteins and RNA.

1

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?8. How do “new” viruses emerge?

- Mutation of an existing virus since there is no proofreading- Spread of an existing virus from 1 host species to another- Spread of viral disease from a small isolated population

9. What is the difference between horizontal & vertical transmission?- Horizontal – 1 organism spreads to another- Vertical – 1 organism inherits disease from parent

10. What are viroids & prions?- Viroids – tiny molecules of naked, circular RNA that infect plants,

several hundred nucleotides long- Prions – infectious proteins (NO genetic material)

- Slow incubation period – at least 10 yrs- Virtually indestructible - 1997 Nobel Prize in Medicine – Stanley Prusiner

The Genetics of Viruses & Bacteria1. What do you know about viruses?2. How big are viruses?3. What are the components of a virus?4. How do viruses identify appropriate cells to infect?5. What is the lytic cycle of a bacteriophage?6. What is the lysogenic cycle of a bacteriophage?7. How do retroviruses (like HIV) reproduce?8. How do “new” viruses emerge?9. What is the difference between horizontal & vertical transmission?10. What are viroids & prions?11. How is bacterial DNA different from eukaryotic DNA? (refer to Ch. 19 notes)

Bacterial EukaryoticCircular chromosome Linear chromosomesNucleoid region NucleusNo introns (all exons) Introns & exonsTranscription coupled w/ translation Transcription & translation separateMore mutations Fewer mutations (proofreading)

12.How does bacterial DNA replicate its circular chromosome?- Figure 16.16

Figure 18.16 Generalized transduction

Phage DNA

Donorcell

Recipientcell

A+ B+

A+ B+

A+

A+ B–

A– B–

A+

Recombinant cell

Crossingover

Phage infects bacterial cell that has alleles A+ and B+

Host DNA (brown) is fragmented, and phage DNA and proteins are made. This is the donor cell.

A bacterial DNA fragment (in this case a fragment withthe A+ allele) may be packaged in a phage capsid.

Phage with the A+ allele from the donor cell infects a recipient A–B– cell, and crossing over (recombination)between donor DNA (brown) and recipient DNA(green) occurs at two places (dotted lines).

The genotype of the resulting recombinant cell (A+B–) differs from the genotypes of both the donor (A+B+) and the recipient (A–B–).

1

2

3

4

5

Figure 18.17 Bacterial conjugation

Sex pilus 1 m

Figure 18.18 Conjugation and recombination in E. coli

1 A cell carrying an F plasmid(an F+ cell) can form amating bridge with an F– celland transfer its F plasmid.

A single strand of the F plasmid breaks at a specific point (tip of blue arrowhead) and begins tomove into the recipient cell. As transfer continues, the donor plasmid rotates(red arrow).

2DNA replication occurs inboth donor and recipientcells, using the single parental strands of the F plasmid as templates to synthesize complementary strands.

3The plasmid in the recipient cell circularizes. Transfer and replication result in a compete F plasmid in each cell. Thus, both cells are now F+.

4

F Plasmid Bacterial chromosome

Bacterial chromosomeF– cell

F+ cell

F+ cell

F+ cell Hfr cell

F factorThe circular F plasmid in an F+ cellcan be integrated into the circularchromosome by a single crossoverevent (dotted line).

1The resulting cell is called an Hfr cell (for High frequency of recombination).

2

Since an Hfr cell has all the F-factor genes, it can form a mating bridge with an F– cell and transfer DNA.

3A single strand of the F factorbreaks and begins to move through the bridge. DNA replication occurs in both donor and recipient cells, resulting in double-stranded DNA

4The location and orientation of the F factor in the donor chromosome determine the sequence of gene transfer during conjugation. In this example, the transfer sequence for four genes is A-B-C-D.

5 The mating bridgeusually breaks well before the entire chromosome and the rest of the F factor are transferred.

6

Two crossovers can result in the exchange of similar (homologous) genes between the transferred chromosome fragment (brown) and the recipient cell’s chromosome (green).

7The piece of DNA ending up outside thebacterial chromosome will eventually be degraded by the cell’s enzymes. The recipient cell now contains a new combination of genes but no F factor; it is a recombinant F– cell.

8

Temporarypartialdiploid

Recombinant F–

bacterium

Conjugation and transfer of an F plasmid from an F+ donor to an F– recipient

(a)

Conjugation and transfer of part of the bacterial chromosome from an Hfr donor to an F– recipient, resulting in recombination

(b)

A+B+ C+

D+

F– cell A–B–

C–

D–

A–B–

C–

D– D–

A–

C–B– D–

A–

C–

B–

A+

B+C+D+A+

B+C+D+A+B+

D+C+

A+

A+

B+

A–B–

C–

D–

A–B+

C–

D–

A+

B+ B–

A+

A+

B+

F+ cell

Mating bridge

Plasmid – extra-chromosomal, small, circular, self-replicating DNA

Figure 18.21 The trp operon: regulated synthesis of repressible enzymes

(a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes.

Genes of operon

Inactiverepressor

Protein

Operator

Polypeptides that make upenzymes for tryptophan synthesis

Promoter

Regulatorygene

RNA polymerase

Start codon Stop codon

Promoter

trp operon

5

3mRNA 5

trpDtrpE trpC trpB trpAtrpRDNA

mRNA

E D C B A

DNA

mRNA

Protein

Tryptophan(corepressor)

Active repressor

No RNA made

Tryptophan present, repressor active, operon off. As tryptophanaccumulates, it inhibits its own production by activating the repressor protein.

(b)

Figure 18.22 The lac operon: regulated synthesis of inducible enzymes

DNA

mRNA

ProteinActiverepressor

RNApolymerase

NoRNAmade

lacZlacl

Regulatorygene

Operator

Promoter

Lactose absent, repressor active, operon off. The lac repressor is innately active, and inthe absence of lactose it switches off the operon by binding to the operator.

(a)

5

3

mRNA 5'

DNA

mRNA

Protein

Allolactose(inducer)

Inactiverepressor

lacl lacz lacY lacA

RNApolymerase

Permease Transacetylase-Galactosidase

5

3

(b) Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.

mRNA 5

lac operon

• Before the invention of antibiotics, the clean modern hospitals of India, which were mostly reserved for Europeans, reported cholera death rates of 86%. Meanwhile, in other more crowded and less hygienic hospitals, the death rate from cholera was only 27%. WHY? Based on knowledge gained from the case study, explain the most likely process that occurred in the crowded hospitals that led to such a low death rate from cholera.

Figure 21.4a, b

Animal development. Most animals go through some variation of the blastula and gastrula stages. The blastula is a sphere of cells surrounding a fluid-filled cavity. The gastrulaforms when a region of the blastula folds inward, creating a tube—a rudimentary gut. Once the animal is mature, differentiation occurs in only a limited way—for the replacement of damaged or lost cells.

Plant development. In plants with seeds, a complete embryo develops within the seed. Morphogenesis, which involves cell division and cell wall expansion rather than cell or tissue movement, occurs throughout the plant’s lifetime. Apical meristems (purple) continuously arise and develop into the various plant organs as the plant grows to an indeterminate size.

Zygote(fertilized egg)

Eight cells Blastula(cross section)

Gastrula(cross section)

Adult animal(sea star)

Cellmovement

Gut

Cell division

Morphogenesis

Observable cell differentiationSeedleaves

Shootapicalmeristem

Rootapicalmeristem

PlantEmbryoinside seed

Two cells Zygote

(fertilized egg)

(a)

(b)

Chapter 21: The Genetic Basis of Development1. How do we study development in the genetics-based lab? 2. How does a zygote transform into an organism?3. How do cells become differentiated?

-All cells have the same DNA, so differential gene expression must be the explanation!

Nucleusremoved

Mammarycell donor

Egg celldonor

Egg cellfrom ovary

Cultured mammary cells are semistarved, arresting the cellcycle and causingdedifferentiation

Nucleus frommammary cell

Grown in cultureEarly embryo

Implanted in uterusof a third sheep

SurrogatemotherEmbryonic

development

Lamb (“Dolly”)genetically identical to mammary cell donor

4

5

6

1 2

3 Cells fused

APPLICATION This method is used to produce cloned animals whose nuclear genes are identical to the donor animal supplying the nucleus.

TECHNIQUE Shown here is the procedure used to produce Dolly, the first reported case of a mammal cloned using the nucleus of a differentiated cell.

RESULTS The cloned animal is identical in appearance and genetic makeup to the donor animal supplying the nucleus, but differs from the egg cell donor and surrogate mother.

Nucleusremoved

Figure 21.7

Chapter 21: The Genetic Basis of Development4. What is a stem cell?

-a relatively unspecialized cell

Figure 21.9

Early human embryoat blastocyst stage

(mammalian equiva-lent of blastula)

From bone marrowin this example

Totipotentcells

Pluripotentcells

Culturedstem cells

Differentcultureconditions

Differenttypes ofdifferentiatedcells

Liver cells Nerve cells Blood cells

Embryonic stem cells Adult stem cells

-can differentiate into cells of different types under specific conditions-Embryonic = totipotent-Adult = pluripotent (can produce some, but not all, cell types)

Chapter 21: The Genetic Basis of Development5. What type of genetic signal leads to cell differentiation?

-Step 1: Cell receives signals from other cells

DNAOFF OFF

OFFmRNA

mRNA mRNA mRNA mRNA

Anothertranscriptionfactor

MyoDMuscle cell(fully differentiated)

MyoD protein(transcriptionfactor)

Myoblast (determined)

Embryonicprecursor cell

Myosin, othermuscle proteins,and cell-cycleblocking proteins

Other muscle-specific genesMaster control gene myoDNucleus

Determination. Signals from othercells lead to activation of a masterregulatory gene called myoD, andthe cell makes MyoD protein, atranscription factor. The cell, nowcalled a myoblast, is irreversiblycommitted to becoming a skeletalmuscle cell.

1

Differentiation. MyoD protein stimulatesthe myoD gene further, and activatesgenes encoding other muscle-specifictranscription factors, which in turn activate genes for muscle proteins. MyoD also turns on genes that block the cell cycle, thus stopping cell division. The nondividing myoblasts fuse to become mature multinucleate muscle cells, alsocalled muscle fibers.

2

-Step 2: A regulatory gene is turned “on”, and a protein is made thatactivates other genes. (“point of no return”)-Step 3: Activated genes make proteins that determine cell type/structure/behavior.

Figure 21.16b

Epidermis

Gonad Anchor cell

Signalprotein

Vulval precursor cells

Inner vulva

Outer vulva

Epidermis

ADULT

Induction of vulval cell types during larvaldevelopment.

(b)

Figure 47.25

EXPERIMENT

RESULTS

CONCLUSION

Spemann and Mangold transplanted a piece of the dorsal lip of a pigmented newt gastrula to the ventral side of the early gastrula of a nonpigmented newt.

During subsequent development, the recipient embryo formed a second notochord and neural tube in the region of the transplant, and eventually most of a second embryo. Examination of the interior of the double embryorevealed that the secondary structures were formed in part from host tissue.

The transplanted dorsal lip was able to induce cells in a different region of the recipient to form structures different from their normal fate. In effect, the dorsal lip “organized” the later development of an entire embryo.

Pigmented gastrula(donor embryo)

Dorsal lip ofblastopore

Nonpigmented gastrula(recipient embryo)

Primary embryo

Secondary (induced) embryoPrimarystructures:

Neural tube

Notochord

Secondarystructures:

Notochord (pigmented cells)

Neural tube (mostly nonpigmented cells)

Chapter 21: The Genetic Basis of Development

-cytoplasmic determinants in the unfertilized egg regulate geneexpression in the zygote that affects differentiation/development

Figure 21.11a

Unfertilized egg cell

Molecules of a a cytoplasmicdeterminant Fertilization

Zygote(fertilized egg)

Mitotic cell division

Two-celledembryo

Cytoplasmic determinants in the egg. The unfertilized egg cell has molecules in its cytoplasm, encoded by the mother’s genes, that influence development. Many of these cytoplasmic determinants, like the two shown here, are unevenly distributed in the egg. After fertilization and mitotic division, the cell nuclei of the embryo are exposed to different sets of cytoplasmic determinants and, as a result, express different genes.

(a)

Nucleus

Chapter 21: The Genetic Basis of Development

-Cytoplasmic determinants from mother’s egg initially establish the axes ofthe body of Drosophila.-bicoid gene

Head

Wild-type larva

Tail Tail

Mutant larva (bicoid)Drosophila larvae with wild-type and bicoid mutant phenotypes. A mutation in the mother’s bicoid gene leads to tail structures at both ends (bottom larva). The numbers refer to the thoracic and abdominal segments that are present.

(a)

T1 T2T3

A1 A2 A3 A4 A5 A6 A7A8

A8A7 A6 A7

A8

Tail

Figure 21.14a

Translation of bicoid mRNAFertilization

Nurse cells Egg cell

bicoid mRNA

Developing egg cell

Bicoid mRNA in mature unfertilized egg

100 µm

Bicoid protein inearly embryo

Anterior end

(b) Gradients of bicoid mRNA and Bicoid protein in normal egg and early embryo.

1

2

3

Figure 21.14b

Chapter 21: The Genetic Basis of Development-7. How does morphogenesis (pattern formation) occur in animals?

After the body’s axes are determined (by cytoplasmic determinants)…-Segmentation genes produce proteins that direct formation of body segments.

Hierarchy of Gene Activity in Early Drosophila Development

Maternal effect genes (egg-polarity genes)

Gap genes

Pair-rule genes

Segment polarity genes

Homeotic genes of the embryo

Other genes of the embryo

Segmentation genesof the embryo

-Then, the development of specific features of the body segments is directedby HOMEOTIC GENES (Hox genes.)

Chapter 21: The Genetic Basis of Development8. What is the relationship among the genetic basis of development across organisms?

-Molecular analysis of the homeotic genes in Drosophila has shown that theyall include a sequence called a homeobox-An identical (or very similar) DNA sequence has been discovered in the homeotic genes of vertebrates and invertebrates

Figure 21.23

Adultfruit fly

Fruit fly embryo(10 hours)

Flychromosome

Mouse chromosomes

Mouse embryo(12 days)

Adult mouse

Chapter 21: The Genetic Basis of Development9. What is apoptosis?

-programmed cell death (cell suicide)Ced-9protein (active)inhibits Ced-4activity

Mitochondrion

Deathsignalreceptor

Ced-4 Ced-3

Inactive proteins

(a) No death signalCed-9(inactive)

Cellformsblebs

Deathsignal

ActiveCed-4

ActiveCed-3

Activationcascade

Otherproteases

Nucleases

(b) Death signal

Figure 21.18 Molecular basis of apoptosis in C. elegans

Chapter 21: The Genetic Basis of Development8. What is apoptosis?

-programmed cell death (cell suicide)-necessary for development of hands/feet in vertebrates

Figure 21.19

Interdigital tissue

1 mm