Biology 203
What three processes lead to the transformation of a zygote into the organism?
Cell division Cell differentiation Morphogenesis
operator:
, in bacterial and phage DNA, is a sequence of nucleotides near the start of an operon to which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon. The operator segment of DNA operates as the "switch."
What percentage of the genes of a typical human cell is expressed at any given time?
20%
regulatory gene
A gene that codes for a regulatory protein, such as a repressor
inducer:
A molecule that binds to and inactivates the repressor, causing it to dissociate from the DNA- binding domain of the operator
virulent phages
A phage that replicates only by a lytic cycle that destroys the host cell
Explain why shorter DNA molecules travel farther down the gel than larger molecules.
As the nucleic acid molecules move, the matrix of agarose fibers impedes the longer molecules more than it does the shorter ones, separating them by length
In prokaryotes, functionally related genes are usually clustered in a single operon. What has been found to be the case in eukaryotes?
Co-expressed eukaryotic genes, such as genes coding for the enzymes of a metabolic pathway, are typically scattered over different chromosomes. coordinate gene expression depends on the association of a specific combination of control elements with every gene of a dispersed group.
What does the name of the flu mean?
H1N1 identifies which forms of the two viral surface proteins are present: hemagglutinin (H) and neuraminidase (N).
What process ensures that all the tissues and organs of an organism are in their characteristic places? Where do the molecular cues that control this process arise
Pattern formation collectively called positional information, are provided by cytoplasmic determinants and inductive signals.
What are the components of a viral envelope?
Phospholipids and membrane proteins, drived from host cell Proteins and glycoproteins Viral origin
What is a retrovirus?
RNA virus that replicates by transcribing its RNA into DNA
Plasmids
Small, circular DNA molecules found in bacteria and in the unicellular eukaryotes called yeasts
operator:
Specific sequence of DNA where the repressor binds.
How many molecules will be produced by four PCR cycles?
The number of moleculesequals 2n, wheren is the number of cycles. 24 = 16
What is a capsid?
The protein shell enclosing the viral genome
Figures 18.7, 18.8, and 18.10 to list the three points at which control of transcription occurs.
Transcription can be controlled by histone modification, such as acetylation and methylation. RNA processing is also a control point at which a variety of transcripts can arise from a single pre-mRNA through the process of alternative splicing. Each unique cell type expresses a specific set of transcription factors called activators that bind to enhancer elements and determine which genes are transcribed.
What property of a virus determines its attachment to a host cell membrane?
a "lock-and-key" fit between viral surface proteins and specific receptor molecules on the outside of cells.
cloning vector?
a DNA molecule that can carry foreign DNA into a host cell and replicate there.
What is an expression vector
a cloning vector that contains a highly active bacterial promoter just upstream of a restriction site where a eukaryotic gene can be inserted in the correct reading frame.
regulatory genes:
a gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes.
What is a pandemic?
a global epidemic
What are four important applications of PCR
a necessary technique in a range of applications: amplification of DNA from organisms for genome sequencing efforts; DNA fingerprinting from blood, tissue, or semen found at crime scenes; amplification of DNA from single cells that are difficult to detect, such as viral-infected cells; and a wide range of applications involving the study of gene expression. It is also often crucial for gene cloning.
proto-oncogenes
a normal cellular gene that has the potential to become an oncogene
What is a prophage?
a phage genome that has been inserted into a specific site on a bacterial chromosome
prophage
a phage genome that has been inserted into a specific site on a bacterial chromosome
restriction site
a short sequence of DNA that is recognized by a specific restriction enzyme and can be utilized as a cloning site for inserting a DNA fragment into a plasmid,
full and complete definition of plasmid.
a small, circular, double-stranded DNA molecule that carries accessory genes separate from those of a bacterial chromosome; in DNA cloning, plasmids are used as vectors carrying up to about 10,000 base pairs (10 kb) of DNA.
promoter:
a specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.
DNA cloning
a technique to produce multiple copies of a particular gene or any other DNA molecule
Explain the three initial steps that occur in cycle 1 of PCR.
a.Denaturation: Heat briefly to separate DNA strands. b. Annealing: Cool to allow primers to form hydrogen bonds with the ends of the target sequence. c. Extension: DNA polymerase adds nucleotides to the 3' ends of each primer
What are three ways bacteria may win the battle against the phages?
a.Natural selection favors bacterial mutants with receptors that are no longer recognized by a particular kind of phage. b. DNA is identified as foreign and cut up by restriction enzymes. 3. Instead of lysing their host cells, many phages coexist with them in a state called lysogeny.
operon genes:
actual coding genes for related proteins. In the lac operon, these genes are involved in uptake and metabolism of lactose.
What are two elements that nearly all animal viruses have
an RNA genome and an envelope
What is the purpose of the primers?
anneal to a specific target sequence and also to provide the DNA polymerase the necessary double-stranded sequence to attach to and begin adding complementary bases to the template at the 3'—OH of the primer
Why don't restriction enzymes destroy the DNA of the bacterial cells that produce them?
bacterial cell's own DNA is methylated in a way that prevents attack by its own restriction enzymes.
restriction enzyme
bacterial endonuclease enzyme that has the ability to recognize and cleave short, specific DNA sequences. evolved to protect bacteria by cutting up foreign DNA from other organisms or phages.
repressor:
binds to the operator and blocks attachment of RNA polymerase to the promoter, preventing transcription of the genes.
Viruses are obligate intracellular parasites. What does this mean?
can replicate only within a host cell.
temperate phages
can undergo a lysogenic cycle, which allows the phage genome to be replicated without destroying the host.
What can lead to these cancer-causing mutations?
chemical carcinogens, X-rays and other high-energy radiation, and some viruses.
What is the role of DNA ligase in this process
covalently bonds the sugar-phosphate backbones of the fragments, whose sticky ends have base-paired
oncogenes
found in viral or cellular genomes that is involved in triggering molecular events that can lead to cancer.
Vaccines
harmless variant or derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen.
DNA technology
main techniques for sequencing and manipulating DNA
biotechnology
manipulation of organisms or their components to produce useful products. It includes selective breeding, genetic engineering, and methods of DNA analysis
What is accomplished in DNA sequencing
the complete nucleotide sequence of a DNA molecule is determined. The color of the florescent tag on each strand indicates the identity of the nucleotide, thereby enabling the sequence of nucleotides as they pass through the capillary to be distinguished by the detector.
What is DNA methylation? What role may it play in gene expression?
the process of adding methyl groups to DNA bases. At least in some species, seems to be essential for the long-term inactivation of genes that occurs during normal cell differentiation in the embryo.
What are sticky ends
the short, single-stranded, overhanging sequences of DNA that can form hydrogen bonds with complementary sticky ends on any other DNA molecules that were cut with the same enzyme.
lysogenic mode of bacteriophage reproduction
the viral genome becomes incorporated into the bacterial host chromosome as a prophage, is replicated along with the chromosome, and does not kill the host.
Why are bacterial plasmids widely used as cloning vectors
they can be readily obtained from commercial suppliers, manipulated to form recombinant plasmids, and then introduced into bacterial cells, and they multiply rapidly owing to the high reproductive rate of their host cells
How do retroviruses, such as HIV, replicate their genome?
transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome
How does a DNA virus reproduce its genome?
use the DNA polymerase of the host cell to synthesize new genomes along the templates provided by the viral DNA.
How do most RNA viruses replicate their genome?
use virally encoded RNA polymerase that can use RNA as a template.
provirus
viral genome that is permanently inserted into a host genome
What are maternal effect genes? Describe some effects they may control
when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offspring's own genotype. certain genes encoded for by the mother are present as cytoplasmic determinants in the egg prior to fertilization and help to establish the axes of the body during early development.
repressor protein
A protein that binds to the operator to block transcription of the operon
The inactive mammalian X chromosome is heavily methylated. What is the result of this methylation?
After an X chromosome is inactivated in a particular cell, all mitotic descendants of that cell have the same inactive X. Thus, if a female is heterozygous for a sex-linked trait (a trait with genes on the X chromosome), about half her cells will express one allele, whereas the others will express the alternative allele.
What portion of a phage enters the host cell? How does it do this?
After the bacteriophage binds to a specific receptor on the outer surface of the host cell, the sheath of the tail contracts, injecting the DNA into the cell and leaving an empty capsid outside.
What are capsomeres?
Capsids built from a large number of protein subunits
Why is the DNA sample to be separated by gel electrophoresis always loaded at the cathode or negative end of the power source?
DNA is a negatively charged molecule due to the phosphate groups the DNA will migrate through the gel matrix toward the positive end of the power source.
Transposons
DNA segments that can move from one location to another within a cell'sgenome
What different shapes may capsids have?
Depending on the type of virus itmay be rod-shaped, polyhedral, or more complex in shape.
How can alternative RNA splicing result in different proteins derived from the same initial RNA transcript?
Different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns. Regulatory proteins specific to cell type control intron-exon choices by binding to regulatory sequences within the primary transcript.
What are the four forms of viral genomes?
Double-stranded DNA, Single-stranded DNA, Double-stranded RNA, Single-stranded RNA
What is meant by host range? Distinguish between a virus with a broad host range and one with an extremely limited host range, and give an example of each.
Each particular virus can infect cells only a limited number of host species. Some viruses have broad host ranges, such as West Nile virus, which can infect mosquitoes, birds, horses, and humans. Other viruses have a host range so narrow that they infect only a single species and are sometimes limited to particular tissue. AIDS virus.
RNA polymerase
Enzyme that transcribes genes of the operon
All genes are not "on" all the time. Using the metabolic needs of E. coli, explain why not.
If the environment of the E. coli cell is lacking in the amino acid tryptophan, the cell responds by activating a metabolic pathway that makes tryptophan from another compound. If the human host eats a tryptophan-rich meal, the bacterial cell stops producing tryptophan, thus saving itself from squandering its resources
What was some early evidence of the existence of viruses? Why were they difficult to study?
In 1883, Adolf Mayer discovered that he could transmit tobacco mosaic disease from plant to plant by rubbing sap extracted from diseased leaves into healthy plants. barely visible under the light microscope.
Compare and contrast the lac operon and the trp operon
In both the lac and trp operons, the entire transcription unit is under the command of one main operator and promoter. The lac operon is an inducible operon for a catabolic (breaking down) process, whereas the trp operon is repressible for an anabolic (building up) process. In both operons, regulation involves negative control of genes because operons are switched off by the active form of the repressor protein.
operon:
The entire stretch of DNA required for uptake and metabolism of lactose
How do different sets of activators come to be present in two cells? Explain how each of these occurs: induction
The molecules conveying inductive signals within the target cell are cell-surface receptors and other proteins expressed by the embryo's own genes. In general, the signaling molecules send a cell down a specific developmental path by causing changes in its gene expression that eventually result in observable cellular changes.
mRNA:
The transcribed product of all genes of the operon.
What are bacteriophages?
a virus that infects bacteria.
What are the two main ways of controlling metabolism in bacterial cells?
a. Cells can adjust the activity of enzymes already present. b. Cells can adjust the production level of certain enzymes; that is, they can regulate the expression of the genes encoding the enzymes.
What are three processes that contribute to the sudden emergence of viruses?
a. The mutations change existing viruses into new strains that can cause disease, even in individuals who are immune to the ancestral virus. b. The dissemination of a viral disease from a small, isolated human population made possible by global travel and other social factors c. The spread of existing viruses from other animals
genetic engineering
direct manipulation of genes for practical purposes
What are restriction enzymes? How do they help prevent viral infection of bacteria?
endonuclease (type of enzyme) that recognizes and cuts DNA molecules foreign to a bacterium (such as phage genomes). The enzyme cuts at specific nucleotide sequences (restriction sites).identify and cut up viral DNA that is detected as foreign.
What are general transcription factors, and how do they function?
essential for the transcription of all protein-coding genes. bind to the TATA box within the promoter and are involved in binding other transcription factors and RNA polymerase II.
What is done in nucleic acid hybridization
exploit the base pairing of one strand of a nucleic acid to the complementary sequence on a strand from another nucleic acid molecule
How can the rate of gene expression be modified by specific transcription factors? (activators or repressors)
greatly increased by activators and can be greatly decreased by repressors. repressors can inhibit transcription by interfering with other activators, others can block transcription by binding directly to control element DNA. Once activators bind to enhancer elements, they interact with other transcription factors and mediator proteins, then recruit RNA polymerase, assembling the transcription initiation complex.
What is the role of an envelope in animal viruses?
helps the virus infect their host.
What important understandings about embryonic development resulted from the research into bicoid?
identification of a specific protein required for determining polarity and position
To demonstrate you understand how the lac and trp operon work, let's assume a human host has had a meal of turkey (rich in the amino acid tryptophan) and washed it down with milk. Explain your answer to each of the following: Will the trp operon be active?
it will be turned off in the presence of abundant tryptophan, thereby preventing the wasting of energy and resources required by the tryptophan biosynthetic pathway.
What are three mechanisms for converting a proto-oncogene to an oncogene?
movement of DNA within the genome, amplification of a proto-oncogene, and point mutations in a control element or in the proto-oncogene itself
What components of the host cell does a virus use to reproduce itself?
nucleotides for making viral nucleic acids, as well as enzymes, ribosomes, tRNAs, amino acids, ATP, and other components needed for making the viral proteins.
Describe the double whammy that results from mutation of p53.
numerous cell-cycle-inhibiting processes will be affected, leading to a higher likelihood of uncontrolled cell growth.
What is an example of a gene of interest that might be engineered into a plasmid
one example is the gene encoding human insulin protein
What is controlled by homeotic genes?
placement and spatial organization of body parts in animals, plants, and fungi by controlling the developmental fate of groups of cells.
Which one are you likely to carry provirus or prophage
provirus
Explain what is meant by epigenetic inheritance, and give an example of epigenetic changes discussed in the text or in class.
refers to inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome. DNA methylation patterns are largely erased and reestablished during gamete formation.
Antiviral drugs
resemble nucleosides and as a result interfere with viral nucleic acid synthesis.
Describe the lytic mode of bacteriophage reproduction
results in the release of new phages by lysis (and death) of the host cell.
four diseases caused by prions and two possible neurodegenerative diseases that may involve prions
scrapie in sheep, mad cow disease, Creutzfeld-Jakob disease, and kuru. Alzheimer's and Parkinson disease
Why are both the gene of interest and the plasmid cut with the same restriction enzyme?
so that both the gene and the plasmid will have the same sticky ends and will be able to be annealed by ligase
What occurs in histone acetylation? How does it affect gene expression?
the attachment of acetyl groups to certain amino acids of histone proteins promotes the folding of chromatin into a more compact structure. As a result, transcribing proteins have easier access to genes in an acetylated region.
How do different sets of activators come to be present in two cells? Explain how each of these occurs: distribution of cytoplasmic determinants
After fertilization, early mitotic divisions distribute the zygote's cytoplasm into separate cells. The nuclei of these cells may thus be exposed to different cytoplasmic determinants, depending on which portions of the zygotic cytoplasm a cell received. The combination of cytoplasmic determinants in a cell helps determine its developmental fate by regulating expression of the cell's genes during the course of cell differentiation.
When a repressor is bound to the operator of the lac operon, is the operon off or on?
Off
Prions
infectious proteins that appear to cause a number of degenerative brain diseases in various animal species.transmitted in food and cause misfolding of proteins, particularly in the brain. The infection results in slow damage but ultimately leads to death.
To demonstrate you understand how the lac and trp operon work, let's assume a human host has had a meal of turkey (rich in the amino acid tryptophan) and washed it down with milk. Explain your answer to each of the following: Will the lac operon be active?
operon is turned off in the absence of lactose (inducer); however, if an abundance of lactose is available, then lactose will bind to the repressor, allowing the transcription of the necessary genes for lactose uptake and metabolism.
