Viruses and Bacteria

1. Viruses and Bacteria What you need to Know Plus Gene Regulation

2. Phage and Bacteria

3. Virus Bacteria Animal Cell

4. Structure of Viruses • Viruses are not cells • Viruses are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

5. Capsids and Envelopes • A capsid is the protein shell that encloses the viral genome • A capsid can have various structures

6. Some viruses have structures have membranous envelopes that help them infect hosts • These viral envelopes surround the capsids of influenza viruses and many other viruses found in animals • Viral envelopes, which are derived from the host cell’s membrane, contain a combination of viral and host cell molecules

8. General Features of Viral Reproductive Cycles • Viruses are obligate intracellular parasites, which means they can reproduce only within a host cell • Each virus has a host range, a limited number of host cells that it can infect • Viruses use enzymes, ribosomes, and small host molecules to synthesize progeny viruses • go to video

9. Reproductive Cycles of Phages • Phages are the best understood of all viruses • Phages have two reproductive mechanisms: the lytic cycle and the lysogenic cycle

10. The Lytic Cycle • The lytic cycle is a phage reproductive cycle that culminates in the death of the host cell • The lytic cycle produces new phages and digests the host’s cell wall, releasing the progeny 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

11. Attachment LE 18-6 Entryof phage DNA and degradation of host DNA Phage assembly Release Head Tail fibers Tails Synthesis of viral genomesand proteins Assembly

12. The Lysogenic Cycle • The lysogenic cycle replicates the phage genome without destroying the host • The viral DNA molecule is incorporated by genetic recombination 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 • Phages that use both the lytic and lysogenic cycles are called temperate phages • Go to video

13. Phage DNA The phage attaches to a host cell and injects its DNA. Daughter cell with prophage LE 18-7 Many cell divisions produce a large 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 Lysogenic cycle The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells. Certain factors determine whether The cell lyses, releasing phages. Lytic cycle is induced Lysogenic cycle is entered or Prophage Phage DNA integrates into the bacterial chromosomes, becoming a prophage. New phage DNA and proteins are synthesized and assembled into phages.

14. Viroids and Prions: The Simplest Infectious Agents • Viroids are circular RNA molecules that infect plants and disrupt their growth • Prions are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals • Prions propagate by converting normal proteins into the prion version

15. LE 18-13 Original prion Prion Manyprions New prion Normal protein

16. The Bacterial Genome and Its Replication • The bacterial chromosome is usually a circular DNA molecule with few associated proteins • Many bacteria also have plasmids, smaller circular DNA molecules that can replicate independently of the chromosome • Bacterial cells divide by binary fission, which is preceded by replication of the chromosome

17. Replication fork Origin of replication LE 18-14 Termination of replication

18. Mutation and Genetic Recombination as Sources of Genetic Variation • Since bacteria can reproduce rapidly, new mutations quickly increase genetic diversity • More genetic diversity arises by recombination of DNA from two different bacterial cells

19. Mechanisms of Gene Transfer and Genetic Recombination in Bacteria • Three processes bring bacterial DNA from different individuals together: • Transformation-Transformation is the alteration of a bacterial cell’s genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment (Griffith) • Transduction -In the process known as transduction, phages carry bacterial genes from one host cell to another • Conjugation -Conjugation is the direct transfer of genetic material between bacterial cells that are temporarily joined (Pili)

20. Transposition of Genetic Elements • The DNA of a cell can also undergo recombination due to movement of transposable elements within the cell’s genome • Transposable elements, often called “jumping genes,” contribute to genetic shuffling in bacteria

21. Transposons • Transposable elements called transposons are longer and more complex than insertion sequences • In addition to DNA required for transposition, transposons have extra genes that “go along for the ride,” such as genes for antibiotic resistance

22. LE 18-19b Transposing Insertion sequence Insertion sequence Antibiotic resistance gene 5¢ 3¢ 3¢ 5¢ Transposase gene Inverted repeat

23. Repressible and Inducible Operons: Two Types of Negative Gene Regulation • A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription • The trp operon is a repressible operon • An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription • The classic example of an inducible operon is the lac operon, which contains genes coding for enzymes in hydrolysis and metabolism of lactose

24. Promoter Regulatory gene Operator LE 18-22a lacl lacZ DNA No RNA made 3¢ mRNA RNA polymerase 5¢ Active repressor Protein Lactose absent, repressor active, operonoff

25. LE 18-22b lac operon lacA DNA lacl lacY lacZ RNA polymerase 3¢ mRNA mRNA 5¢ 5¢ Transacetylase Permease -Galactosidase Protein Inactive repressor Allolactose (inducer) Lactose present, repressor inactive, operon on

26. Inducible enzymes usually function in catabolic pathways • Repressible enzymes usually function in anabolic pathways • Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor

27. Positive Gene Regulation • Some operons are also subject to positive control through a stimulatory activator protein, such as catabolite activator protein (CAP) • When glucose (a preferred food source of E. coli ) is scarce, the lac operon is activated by the binding of CAP • When glucose levels increase, CAP detaches from the lac operon, turning it off

28. Promoter LE 18-23a DNA lacl lacZ RNA polymerase can bind and transcribe Operator CAP-binding site Active CAP cAMP Inactive lac repressor Inactive CAP Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized

29. Promoter LE 18-23b DNA lacl lacZ CAP-binding site Operator RNA polymerase can’t bind Inactive CAP Inactive lac repressor Lactose present, glucose present (cAMP level low): little lac mRNA synthesized

30. LE 19-2a 2 nm DNA double helix Histone tails His- tones Histone H1 10 nm Nucleosome (“bead”) Linker DNA (“string”) Nucleosomes (10-nm fiber)

31. LE 19-2b 30 nm Nucleosome 30-nm fiber

32. LE 19-2c Protein scaffold Loops 300 nm Scaffold Looped domains (300-nm fiber)

33. Concept 19.2: Gene expression can be regulated at any stage, but the key step is transcription • All organisms must regulate which genes are expressed at any given time • A multicellular organism’s cells undergo cell differentiation, specialization in form and function

34. Differential Gene Expression • Differences between cell types result from differential gene expression, the expression of different genes by cells within the same genome • In each type of differentiated cell, a unique subset of genes is expressed • Many key stages of gene expression can be regulated in eukaryotic cells

35. Regulation of Chromatin Structure • Genes within highly packed heterochromatin are usually not expressed • Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression

36. Histone Modification • In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails • This process seems to loosen chromatin structure, thereby promoting the initiation of transcription

37. LE 19-4 Histone tails DNA double helix Amino acids available for chemical modification Histone tails protrude outward from a nucleosome Unacetylated histones Acetylated histones Acetylation of histone tails promotes loose chromatin structure that permits transcription

38. DNA Methylation • DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species • In some species, DNA methylation causes long-term inactivation of genes in cellular differentiation • In genomic imprinting, methylation turns off either the maternal or paternal alleles of certain genes at the start of development