AP BIO chapter 18/19 test

study the lyctic cycle on 396 and be sure you can describe it in detail

1. Lyctic cycle is induced 2. New phage DNA and proteins are synthesized and self-assemble into phages 3. The cell lyses, releasing phages 4. the phage attaches to a host cell and injects its DNA

Describe the lysogenic cycle

1. Phage DNA integrates into the bacterial chromosome, becoming a prophage 2. The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells 3. many cell divisions produce a large population of bacteria infected with the prophage 4. Daughter cell prophage 5. Occasionally, a prophage exists the bacterial chromsome initiating a lyctic cycle.

Describe the four types of viral structure

1. Tabacco mosiac Virus has a helical capsid with the overall shape of a rigid rod (RNA curled up) 18x 250 nm 2. Adenoviruses have an isosahedral capsid with a glycoprotein spike at each vertex (corner) 70-90 nm 3. Influenza viruses have eight different RNA molecules, each wrapped in a helical capsid, and an outer envelope studded with glycoprotein spikes 80-200 nm 4. Bacteriophage T4,likeother 'T-even' phages, has a complex capsid consisting of an icosahedral head and a tail apparatus 80 x 225 nm

what are the sources of developmental information for the early embryo?

1. cytoplasmic determinants in the egg The unfertilized egg 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 miotic division, the cell nuclei of the embryo are exposed to different sets of cytoplasmic determinants and, as a result, express different genes. 2.induction by nearby cells Cells at the bottom of the early embryo are releasing molecules that signal (induce) nearby cells to change their gene expression

2 sources of information affect transcription in developing embryos:

1. cytoplasmic differences in the unfertilized egg (cytoplasmic determinants) 2. signals from other cells (induction) Once an embryonic cell has recited enough signals, it undergoes determination such that even though it appears undifferentiated, its development fate has been fixed (or determined). Consider moD example from 379. Note that one of the regulatory targets of the MyoD proteins (acting as a transcription factors) is the myoD gene itself; thus, this gene's activity is self-perpetuating once begun

structural genes, 2 examples

1. galactosidase: enzyme that breaks lactose down into glucose and galactose 2. permeate- transport protein in membrane that allows lactose to enter cell easily

Describe the replicative cycle of an enveloped RNA virus

1. glycoproteins on the viral envelope bind to specific receptor molecules on the host cell, promoting viral uptake by the cell 2. The capsid and the viral genome enter the cell. Degredation of the capsid by cellular digestive enzymes causes the release of viral genetic material into the cytosol of the cell 3. The viral genome functions as a template for complementary RNA production by viral RNA polymerase 4. New copies of viral genome RNA using the complementary RNA strands as templates 5. Complementary RNA strands also serve as mRNA, which is translated both in to capsid proteins and glycoproteins for the viral envelope (in the ER and Golgi apparatus) 6. Vesicles transport envelope glycoproteins to the plasma membrane 7. a capsid assembles around each viral genome molecule 8. Each new virus buds from the cell, its envelope studded with viral glycoproteins embedded in membrane derived from the host cell

Emerging viruses include HIV, ebola, SARS, EEE and West Nile virus. Viral diseases are not treatable with antibiotics and sometimes are not treatable at all. List the 3 processes that contribute to emergence of new viral diseases

1. mutation of existing viruses (RNA polymerase have high error rate) 2. the dissemination of a viral disease from a small, isolated, human population 3. the spread of existing viruses from other animals (3/4 originate this way)

why have phages not driven bacteria to extinction

1. natural selection drives fluxes constantly in the parasite/host relationship 2. restriction enzymes 3. lysogeny

Describe development from egg to larva for Drosophila

1. the egg is surrounded by support cells (follicle cells) within one of the mother's ovaries 2. The developing egg enlarges as nutrients and mRNAs are supplied to it by other support cells (nurse cells), which shrink. Eventually the mature egg fills the egg shell that is secreated by the follicle cells. 3. The egg is fertilized within the mother and then laid 4. A segmented embryo and then 5. a larva

on average, each enhancer region has about

10 control elements, each of which may be able to bind to 1-2 different transcription factors (which can be activators or repressors)

Define a vaccine. Against what kinds of viral infections are vaccines effective?

A harmless variant or derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen. Those with a narrow host range, emerging viruses.

prophage

A phage genome that has been inserted into a specific site on a bacterial chromosome

Describe the replicative cycle of a retrovirus (like HIV), and define retrovirus

A retrovirus reverses the role of DNA to RNA into RNA to DNA in the host cell 1. The envelope glycoproteins enable the virus to bind to the cell's specific receptor proteins 2. The virus fuses with the cellular membrane. the capsid proteins are removed, releasing the viral proteins and DNA into the cytosol of the host cell 3. Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA 4. Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first 5. The double stranded DNA is incorporated into the cellular genome as a provirus 6. Proviral genes are transcribed into RNA molecules, which serve as genomes for progeny viruses and as mRNA for translation into viral proteins 7. The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope proteins (made in the ER) 8. vesicles transport glycoproteins to the cell's plasma membrane 9. Capsids are assembled around viral genomes and reverse transcriptase molecules 10. New viruses, with viral envelope glycoproteins bud from the host cell

provirus

A viral genome that is permanently inserted into a host genome (HIV)

Describe a model for the action of enhancers, DNA bending protein, and transcription activators

Activator proteins bind to distal control elements grouped as an enhancer in the DNA. This enhancer has three binding sites, each called a distal control element. A DNA bending protein brings the bound activators closer to the promoter. General transcription factors, mediator proteins, and RNA polymeraseII are nearby. The activators bind to certain mediator proteins and general transcription factors, helping them form an active transcription initiation complex on the promoter. Bending of the DNA by a protein enables enhancers to influence a promoter hundreds or even thousands of nucleotides away. Specific transcription factors called activators bind to the enhancer DNA sequences and then to a group of mediator proteins, which in turn bind to GTFs and ultamately RNA polymerase II, assembling the transcription initiation complex. These protein-protein interactoins facilitate the correct positioning of the complex on the promoter and the initiation of RNA synthesis. Only one enhancer is shown here, but a gene may have several enhancers that act at different times or in different cell types.

what is reverse transcriptase and what is its role in retroviral reproductive cycles?

An enzyme that is encoded by certain viruses (retroviruses) that uses RNA as a template for DNA synthesis RNA to DNA flow

why are these 3 genes controlled as a unit?

Because the bacteria never need just one of them; if one is needed then all are needed. The operon ensure that they are transcribed and translated as a group this is more efficient for the cell, and conserves resources

mi RNA and siRNA role in post transcriptional controls

Both miRNAs and siRNAs are small, single stranded RNAs that associate with a complex of proteins and then can base pair with mRNAs that have a complementary sequence. This base pairing leads to either degradation of the mRNA or blockage of its translation. In some yeasts, siRNAs associated with proteins in a different complex can bind to back centromeric chromatin, receipting enzymes that cause condensation of that chromatin into heterochromatin. Both miRNAs and siRNAs are processed from double stranded RNA precursors, but have subtle differences in the structure of those precursors.

How does a mutation in this gene lead to legs being produced instead of antennae on the fly's head?

Development defects in regulatory genes The mutated gene encodes a transcription factor that regulates other genes and its malfunction leads to misplaced structures, such as legs instead of antennae

these proteins (polycomb group proteins) were first found and studied in

Drosophila but now are known in all kinds of animals; most active mouse and human genes have H3k4me3 surrounding their promoters

What is "evo-devo" and how does it relate to the pitx-1 example?

Evo-Devo is a combination of two disciplines within the field of biology: evolutionary biology and developmental biology The mutations in developemental (regulatory) genes leads to changes in phenotype; this is either selected for or against-contributing to an evolution of the species

Discribe the lac operon in E. Coli, when lactose is absent and when lactose is present

LACTOSE ABSENT The repressor is active, operon off: The lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator LACTOSE PRESENT The repressor is inactive,operon on: Allolactase, an isomer of lactose derepresses the operon by inactivating the repressor.In this way, the enzymes for lactose utilization are induced (lacZ, lacY,lacA = beta galactosidase, permeate,transacetylase) E coli uses these three enzymes to take up lactose from the environment and metabolize it, the genes for which are clustered in the lac operon. The first gene, lacZ codes for B galactosidase, which hydrolyzes lactose to glucose and galactose. The second, lacY codes for permease, the transport protein which transports lactose into the cell. The third, lacA, codes for transacetylase, whose function is unclear. Unusually, the gene for the lac repressor, lacI, is adjacent to the lac operon (allosteric regulation)

Describe differentiation in detail, using myoD pathway as an example

MyoD protein stimulated the myoD gene further and activates genes encoding other muscle-specific transcription factors, which in turn activate genes for muscle proteins. MyoD also turns on genes that block the cell cycle, thus stopping cell division. The non dividing myoblasts fuse to become mature multinucleate muscle cells, also called fibers.

Describe determination in detail, using myoD pathway as an example

Signals from other cells lead to activation of a master regulatory gene called myoD, and the cell makes MyoD protein, a specific transcription factor that acts as an activator. The cell, now called a myoblast, is irreversibly committed to becoming a skeletal muscle cell

describe the trp operon in E Coli; regulated synthesis repressible enzymes when tryptophan is absent/present

TRYPTOPHAN ABSENT repressor inactive, operon on: RNA polymerase attaches to the DNA at the operon's promoter and transcribes the operon's genes. TRYPORTHAN PRESENT As tryptophan accumulates, it inhibits its own production by activating the repressor protein, which binds to the operator, blocking transcription until the tryptophan bound is used by the cell Tryptophan is a amino acid produced by an anabolic pathway catalyzed by repressible enzymes. a) the five genes encoding the polypeptide subunits of the enzymes in this pathway are grouped, along with a promoter, into the trp operon. The trp operator (the repressor binding site) is located within the top promoter (the RNA pol binding site).Accumulation of the tryptophan, the end product of this pathway, represses transcription of the trp operon, thus blocking synthesis of all the enzymes in the pathway and shutting down tryptophan production.

describe a simplified viral reproductive cycle

The virus enters the cell and is uncoated, releasing viral DNA and capsid proteins. Host enzymes replicate the viral genome. Meanwhile, host enzymes transcribe the oral genome into viral mRNA, which host ribosomes use to make more capsid proteins. Viral genomes and capsid proteins self-assemble into new virus particles, which exit the cell. A virus is an intracellular parasite that uses the equipment and small molecules of its host cell to replicate. In this simplest of viral cycles, the parasite is a DNA virus with a capsid consisting of a single type of protein

what is meant by a virus' host range? Is there is a "cellular" host range, too?

Viral host range: each particular virus can infect cells of only a limited number of host species. The host specificity result from the evolution of recognition systems by the virus. Yes can only be infected by some viruses

How did/do new viruses originate? What evidence supports this view?

Viruses originated from naked bits of cellular nucleic acids that moved from one cell to another, perhaps via injured cell surfaces. Mimiviruses included genes previously found only in cellular genomes. "Still an unresolved question"

define prophage

a phage genome that has been inserted into a specific site on bacterial chromosomes; may lyse itself from the DNA to initiate the lyctic cycle

define a virulent phage

a phage that replicated only by alyctic cycle

define vivroid

a plant pathogen consisting of a mol. of a naked, circular DNA a few hundred nucleotides long

transcriptional controls

a. alternative RNA splicing for alternate proteins or finer regulation b. degradation of mRNA (note roles of mi RNA and siRNA) in minutes for proks. vs hours/days/weeks for euks c. control of protein translation i. e.g. no poly-A tails added to egg mRNA until after fertilization or ii. regulatory proteins that bind to 5'UTR and block ribosome binding or iii. activation of required translation factors d. protein processing to produce functional proteins e. protein degration- after ubiquitin is added to target proteins, the proteins are destroyed in proteasome complexes ADCPD

negative control:

a. negative controls occurs via blocking of the operator by the repressor; as long as there is no lactose in the medium then the repressor stays bound and transcription is blocked

degree of condensation of DNA

a. transcription rates are affected by "location of a gene's promoter relative to nucleosomes and to the sites where the DNA attaches to the chromosome scaffold or nuclear lamina" b. highly condensed heterochromatin not accessible to transcription enzymes (e.g. telomeres, centromeres, most of Barr bodies) c. more spread out euchromatin is accessible to transcription enzymes

b. Pattern formation in drosophila process

a/ maternal effect genes (egg-polarity genes)-if these genes are mutant in the mother then the embryo is affected regardless of its genotype a. establish anterior-posterior acts and dorsal central acts. WHAT DOES THIS STATEMENT MEAN? b. are passed from the mother to the egg in the form of mRNA in nurse cells c. e.g. bicoid mRNA is passed from nurse cells at the anterior end of the egg i. bicoid mRNA becomes anchored to the cytoskeleton at the anterior end ii. bicoid mRNA is transcribed after fertilization to produce a protein that diffuses away from the anterior end to set up a concentration gradient iii. bicoid protein deactivate caudate mRNA and increase transcription of hunchback (anterior gap gene) iv. areas injected with high concentrations of bicoid mRNA develop anterior structures wherever bicoid is injected

repressors can also bind to

activators to block their binding to DNA or can recruit deacetylation enzymes

repressible

active all the time except when building material is already present in environment

(DNA modification) after DNA replication is complete methylating enzymes

add methyl groups on new stands according to the methylation patterns on the original strands (mechanism of epidemic regulation and genomic imprinting)

when lactose is present...

allolactose is made and binds to the repressor, induces a shape change and prevents the repressor from binding to the operator

combinatorial control of gene activation with multiple activators/repressors

allows fine transcriptional control over which genes are active in which cells at any given stage of development because there are so many possible combination of the 12 or so control elements

(histone modification) acetylation enzymes may

also bind and recruit transcription factors and vice versa!i. some acetylation/deacetylation enzymes bind to or part of transcription factors

what determines whether a given virus enters the lytic vs. the lysogenic cycle?

an environmental signal (radiation/chemicals) or lack of lyso.

define prion

an infection aged that is a misfiled version of a normal cellular protein. Prions appear to increase in number by converting correctly folded versions of the protein to more prions

what are the three axis in early development?

anterior to posterior right to left dorsal to ventral

describe cell specific transcription, using two examples to illustrate your point

both liver cells and lens cells have the genes for making the proteins albumin and crystallin but only liver cells make albumin (a blood protein) and only lens cells make crystallin (the main protein of the lens of the eye). The specific transcription factors (activators) made in a cell determine which genes are expressed. Each enhancer has a unique combination of elements. All the activator proteins required for high level expression of the albumin gene are present only in liver cells, wheras the activators needed for expression of the crystallin gene are present only in lens cells. For simplicity, we consider only the role of specific transcription factors that are activators here, although repressors may also influence transcription in certain cell types.

what is required for viral reproduction?

by injecting its genetic information into a cell a single virus hijacks a cell, requiting cellular machinery to manufacture many new viruses and promote further infection

(histone modification) methylation of histones

can lead to chromatin condensation ex: methylation of lysine at position 9 and 27 of H3 BUT methylation of lysine 4 on H3 up regulates transcription and there can be 1-3 methyls per lysine on these histones; hence a "methylation code"!

what are restriction enzymes and why are they made?

cellular enzymes made to cute up possibly infect us foreign DNA/RNA

(transcription factors and eukaryotic gene structure) transcription requires

coordinate between TBP, RNA pol ii and transcription factors to form a transcription initiation complex at the promoter made up of general transcription factors (such as Tata binding proteins-TBP) and mediator proteins

(histone modification) addition of phosphate groups to histone AA's can lead to

euchromatin formation and gene activation

morphogenes

from other gradients to establish aces and appropriate structures; note that these morphogens are all transcription factors

regulator gene

gene that makes repressor protein (not part of operon)

note the difference between general and specific transcription factors on page 369

general transcription factors are needed for all RNA production, these lead to a low rate of initiation and production of few RNA transcripts. In eukaryotes, high levels of transcription of particular genes at the appropriate time and place depend on the interaction of control elements with another set of proteins, specific transcription factors

high glucose levels---->

high ATP and low cAMP

(DNA modification)proteins that bind to methylated C's recuit

histone deacylation enzymes

advantage to neg control when lactose is not present

if here is no lactose to digest then bacteria that make these proteins anyway will not compete very well with bacteria that do not make these proteins

inducible

inactive except when metabolite is present

example of polycomb group proteins (PcG) shut down

lineage specific in ES(Embryonic Stem0 cells by trimethylating H3K27 (where K=lysine ). As these cells differentiate into Neural stem cells, an H3K27me3 demethylase enzyme is activated and reactivates these lineage specific genes. Descendants of these NS cells will have the same level of demethylated H3k27 genes and thus the same genes will be in the form of euchromatin and available for expression

these mediator proteins

link activator proteins bound to enhancer regions of DNA to the promoter and RNA pol II. Note: the enhancer regions may be quite distant and may be in introns and that DNA bending proteins allow the distal control element to contact the promoter

capsids are made of

lots of copies of a few (or only one) protein subunits called capsomeres; note the different viral structures on 394

low glucose levels----->

low ATP and high cAMP

cytoplasmic determinants

maternal substances in the egg that influence the course of early development

positional information

molecular signals that locate a cell in relation to the anterior-posterior acts and the dorsal-ventral acts AND that control the differentiation of a cell and its offspring 2. homeotic genes specify segment identity!!!!!!!!!!!!!!!!!!!!!!!!!!!!

when cAMP levels are high

more cAMP binds to CAP (a protein that is always present) to form the cAMP/CAP complex

"Any give gene may have

multiple enhancers, each active at a different time or in a different cell type or location in the organism." example: pitx1gene has 3 different enhancers one active in the jaws, one active in the pituitary, and one active in hindlimb region, each at different times in the development of the vertebrate

coordinately controlled genes may be

near each other on chromosomes in clusters of genes that each have their own promtoers and transcriptional control....but are condensed or uncondensed together// or may have the same specific transcription factors with the same control elements so that all the genes with the same control elements are expressed together "no matter where they are in the genome" a. example: estrogen/protein receptor complex that binds to a variety of genes that move uterine cells throughout the cell cycle to allow uterine wall to thicken in preparation for implantation

cell division

necessary to produce enough cells oto differentiate and shape into a functional body with specialized cells and organs

viral structure

nucleic acid (and sometimes a few enzymes) inside a protein capsid (note that enveloped viruses also have an outer layer of host cell membrane with viral proteins and glycoproteins)

postive control:

positive control occurs via changes in the promoter that actively increase so the operator is not blocked by the repressor

repressor proteins

protein that binds to the operator to prevent RNA pol from moving from promoter to structural genes

explain the difference between a provirus and a prophage

provirus never leaves, prophage does at the start of the lyctic cycle

(DNA modification) methylation of bases (mainly Cytosines)

reduces rate of transcription.

promoter

region of DNA to which RNA pol binds to begin transcription

operator

region of DNA to which repressor protein binds to block transcription

epigenetic inheritance

regulated inheritance of traits via changes not in DNA sequence but of its transcription (another definition: "additional information superimposed on the genome that contributes to the heritable establishment and maintenance of transcriptional states and cellular identity."

e. what kind of gene is the antennapdeia gene from fig. 18.20?

regulatory gene mutations in certain regulatory genes, called homeotic genes cause abnormal placement of structures in an animal. (Homeotic mutant: mutation of a single gene)

nucleic acids may be in

ring or linear form and have as few as 4 or as many as 1000 genes; note that bacterial genomes range from 200 to a few thousand genes

homeotic genes

specify segment identity

(histone modification) acetylation of N-terminus histone tails leads to

spreading out of chromatin due to neutralization of positive charges on histone R groups so that histone tails don't bind to nearby nucleosomes (result 10 nm fibers and not 30 nm fibers)

study the lysogenic/lystic cycles on 397 and res sure you can describe them in detail and define a temperature phage

temperate phage: phages capable of using both modes of replicating within a cell (coexists with host cells)

ploy comb group proteins (PcG)

tend to shut down lineage-specific genes in undifferentiated cells by methylating H3K9 and H3K27 while Trithorax group (TrxG) proteins up-regulate transcription by try-methylating H3K4 to H3K4me3

when this cAMP/CAP complex binds to the promoter..

the affinity of the promoter for RNA pol increase and so does the rate of transcription

pattern formation

the building of a functional body in 3 dimensional space such that organs and structures develop where they belong

differentiation

the process by which cells become specialized in structure and function. You have over 200 different cell types, yet all have the same DNA sets

morphogenesis

the sculpting of masses of differentiating cells into larger, complex structures such as limbs, organs, organ systems (respiratory or digestive) or skin

adv. if lactose is present and glucose feels are low

then and only then is lactose the cheapest energy source for the bacteria; cAMP levels are the inverse f glucose levels and automatically allow the bacteria to respond optimally to changes in sugar availability

are viruses alive? explain your answer

viruses cannot reproduce or carry out metabolism outside of a host cell. most biologists agree they are not alive but exist in a shady area between life forms and chemicals. Viruses lead a "borrowed life"

What is required for a virus to invade a reproduce inside a host cell?

viruses identify host cells by a "lock and key" fit between viral surface proteins and specific receptor mols. on the outside of cells