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

Phage and Bacteria

Virus Bacteria Animal Cell

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

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

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

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

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

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

LE 18-6 Attachment Entry of phage DNA and degradation of host DNA Phage assembly Release Head Tails Tail fibers Assembly 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 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

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

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

LE 18-13 Original prion Prion Many prions New prion Normal protein

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

LE 18-14 Replication fork Origin of replication Termination

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

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)

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

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

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

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

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

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

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

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

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

Lactose present, glucose present (cAMP level low): little lac LE 18-23b Promoter 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

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

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

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

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

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

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

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

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

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