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Micro Exam 2
Terms in this set (97)
__________ is the process of moving a transposable element within or between DNA molecules.
A missense mutation may generate:
no phenotypic change
a loss-of-function mutation
a gain-of-function mutation
Why is recombination advantageous?
-It allows cells to use DNA donated by others of the same species to repair their damaged genes.
-It gives the ability to enhance the competitive fitness of the cell.
-It is an internal method of DNA repair.
In __________ the number of genes transferred is limited by the size of the phage head.
During conjugation the DNA passes through the __________, NOT the __________.
Horizontal gene transfer can occur via
Which of the following is a mutation?
- harmful deletion of part of an organism's DNA.
- A single base change that enhances fitness.
- A change in the DNA that does not change protein structure.
Which of the following is a laboratory technique for inducing transformation?
Which type of DNA uptake is dependent on transferable plasmids?
Overtime, the genome of a species
May change due to mutation or gene swapping
An insertion sequence contains a gene for which enzyme?
In the Basic Ames test for mutagenesis, a mutagen is tested to see if it can
produce colonies on basic medium that lacks histidine, starting with a his mutant strain of bacteria
__________ RNAs bind to complementary sequences of target transcripts and stimulate or prevent translation.
When __________ interacts with RNA polymerase, it increases the rate of transcription initiation of the lac operon.
cAMP receptor protein
A transmembrane sensor kinase protein senses an environmental condition outside __________ bacteria or in the periplasm of a/an __________ bacteria.
The lac operon will be maximally transcribed when
lactose is present but glucose is not
Similar to the trp operon, the genes encoding proteins for histidine synthesis are in a his operon that is under attenuation control.
The his operon leader sequence probably contains several His codons in a row
Which of the following is composed of DNA?
A DNA microchip, scanned with cDNAs, can give information about
the transcription of specific genes
In attenuation occurring at the trp operon, when will the ribosome pause at the leader sequence?
when tryptophan levels are low
Quorum sensing may be involved in which of the following processes?
- Bacterial luciferase expression
- Control of bacterial virulence genes
- Nitrogen-fixing bacterial symbiosis with plants
Which of the following is least subject to change in the cell? Genome, transcriptome, or proteome
Molecules of sRNA do not encode proteins but are used to __________ the translation of specific mRNAs into proteins
Which of the following can cause transcription to end?
- stem and loop
- stop codon
In prokaryotic cells
Transcription and translation occur in the same compartment at the same time
When a genome is annotated, it means that
an attempt has been made to locate all the genes in the genome
An open reading frame (ORF) encodes for
The entire complement of RNA produced under a given set of conditions is called a(n)
The very first DNA sequencing technology called the Sanger method relies on
the incorporation of dideoxynucleotides that terminate chain extension during DNA synthesis
Which one of the followings is NOT an example of quorum sensing?
1. flagellar rotaation switching
2. virulence factor production in Staphylococcus aureus
3. light production in biolumenscent bacteria of the Bobtail squid light organ
4. light production vibrio bacteria
flagellar rotaation switching
Reverse transcriptase is a(n)
RNA-dependent DNA polymerase
The term "phage" is generally reserved for the viruses that infect
SOS regulatory system is activated by
Microarrays allow for
- the analysis of global gene expression.
- the hybridization of cDNA (converted from mRNA) with DNA affixed to a solid-state support.
- a comparison of expression of different genes under different growth conditions.
A virus that kills its host is said to be
lytic or virulent
True or False: Lysogeny is unique to bacteriophages; similar relationships have not been found among the animal viruses.
Compared to the number of antibiotics, the number of antiviral drugs is small because
viruses use host cell machinery to replicate
6.1 Main Idea
Small viruses were the first organisms whose genomes were sequenced, but now many prokaryotic and eukaryotic cellular genomes have been sequenced.
6.2 Main idea
DNA sequencing tech. is advancing very quickly. The original Sanger method is rarely used and tere are now four successive generations of sequencing tech. Advances in tech. have greatly increased the speed of DNA sequencing. Shotgun techniques employ random cloning and sequencing of small genome fragments followed by computer generated assembly of the genome
6.3 Main Idea
Computer analysis of sequencing data is a vital part of genomics
virtually all eukaryotic cells contain mitochondria and in addaion plant cells contain chloroplasts. both organelles contain circular dna geonomes that encode rRNA, tRNA, and few proteins needed for metabolism
Microarrays consist of genes or gene fragments attached to a solid support in a known patern; mRNA is then hybridized with the DNA to determine patterns of gene expression. the arrays are large enough got the transcription pattern of an entire genome (the transcriptome) to be analyized
Proteomics is the analysis of all the proteins present in an organism. the ulitmate aim iof proteomics is to undeerstand the structure, fucntion, and regulation of these proteins. the interactome is the total set of interactions between macromoleciles inside the cell
Most microorganisms in the environment have never been cultured. nonehteless. analusos of ddna smaples has revealed enormous seqeunce diversity in most habitats. the concept of the metagenome embraces the total genetic content of all the oragiams in a particular habitat
Organisms may aquire genes from other organisms in their environemnet by horizontal gene transfer, and such tranfer may cross phylogeneic domain boundaries. Mobile DNA elements like transposons intergrons, and viruses, str important in genome evlution and often carry genes encodeing antibiotic resistance or virtulence factors
Most genes encode proteins and most proteins are enzymes. expression of an enzyme encoding gene is regulated by controlling yhe activiry of the enzyme or controlling the amount of enzyme prodcued
certain proteins bind to DNA when speicific domains of the protein bind to speicific regions of the dna molecule. in most cases the interactions are sequence specific. proteins that bind to DNA are often regulatory proteins that effect gene expression.
the amount of a specific enzyme in a cell can be controlled by regualtory proteins that bind to DNA and increase (induce) or decrease (repress) tje amount of messenger RNA that encoddes the enzyme. in NEgative control of transcription, the regulatory protein is claled a repressor and it inhibits mRNA sythesis
postiive regulators are called activator proteins. they bind to activator binding sites on the DNA and stimulate transctopriom. inducers modify the activity of the avtivating proteins. in postive control of enzyme induction, the inducer promotes the binding of the activator protein and thiss stimuates transcrption
Global control systems regulate the epression of many genes. the lac operon is under catabolite repression as well as its own specific negative regulatory system
archaea and bacteria use DNA binding activator and repressor proteins to regulate gene expression at the level of transcription
Signal transduction systems transmit environmental signals to the cell. In prokaryotes, signal transduction si typically carried out by a two component regulatory system that includes a membrane integrated sensor kinase and a cytoplasmic response regulator (acitivty of regualtor depends on phosphorylation)
quorum sensing allows cells to monitor their environment for cells of their own kind. quorum sensing depends on the sharing of speicial small milecules known as autoinducers. once a sufficient concentration of the autoinducer is present, specific gene expression is triggered
Attenuation is a mechanism whereby transcription is controlled after initation of mRNA synthesis. attenutation mechanisms depend upon stem-loop structures in the mRNA
a virus is an intracellular parasite that requires a suitable host cell for replication. A virion is the extracellular form of a virus and contains either an RNA or a DNA genome inside a protein shell. Once inside the cell, either the virion or its nucleic acid redirects host metabolism to support virus replication. Viruses are classified by the characteristics of their genome and hosts. Bacteriophages infect bacterial cells.
In the virion of a naked virus only nucelic acid and protein are present
The attachment of a virion to a host cell is highly specific process. recognition proteins on the virus recognize speicifc receptors oj the host cell. someties the entire virion enters the hose cell, whereas in other case, as with msot bacteriophafes only the viral genome enters
Bacteriophage T4 cotnains a double stranded DNA genome that is both circularly permuted and terminally redundant. T4 encodes its own DNA polymerase and several other replication proteins. cells emply resitriciton enzymes on attempts to destroy viral and other froeighn DNA but T4 has chemically modified its DNA to amke ot resistant to such attack. Cells also modify their own DNA to protect it form their own restriction enzymes
Some bacteriophages are temperate menaing that they can initiate lytic events or integrate into the host genome as a prophage. this initaites a state called ltsofenct in which the virus does not destroy the cell. virus can decide if lytic or lysogenic depending on environment
Retrovirus like AIDS viruses are RNA virusestbat employ enzyme reverse transcriptase to replicate their RNA genome through a DNA intermediate. The DNA can then integrate into the host chromosomes where it can later be transcribed to yield a viral mRNA and genomic RNA
number of viruses on earth is greater than number of cells by 10 fold. most of earths genetic diversity resides in virus genomes
some viruses employ reverse transcirptase incliding retroviruses
viroids are circular sigle standed rna moleciles that do not encode proteins and are dependenet on host encoded enzymes for replication. unlike viruses viriouds are not enclosed woth a capsid (protein coat) anf all known viroids are plant pathogens
prions consist of protein but have no nucleic acid of any kind
mutation is a heritable change in DNA swuence and may lead to a change in phenotype. selectable mutations are those that give mutant a growth advantage under environmental conditions and are helpful in research. if selection is not possible mutants must be identifed by screening
mutations; spontaous or induced are in the vase sequence of nucleic acid in a genome. a point mutation is due to single base pair change. etc
RNA genomes = more mutations than DNA
mutagens are chemical physical or biologial afents that increase the mutation rate. mutagens can alter DNA in many different ways. however alterations in NDA are not mutations unless they are inherited, some DNA damage can lead to cell death if not repaired
homologous recombination occurs only when closely related DNA squences from 2 distinct genetic elemetns are combined togeher in a single element. recombination is an impotant evolutionary process and cells have speicific mechanisms for ensure that recombination takes place
transduction is the transfer of host genes from one bacterium to another by a bacterial virus. in generalized transuction defective virus particles randomly incorpporate fraements of the cells chromosomal DNA but the transducing efficiency is low. in specialized transicction the NDA of a temperate cisrus excises incorrectly and takes adjacent host genes along woth it; trtanducing efficiency can be high
Conjugation is a mechanism of DNA tranfsger in prokaryotes that requires cell to cell contact. vconjugation is controlle dby genes carrued by certain plasmids sucg as F plasmid and requires trasfer of the plasmid from a donor cell to a recipient cell. Plasmid DNa transfer requires replciarion using the rolling circle mechanism
transposons and inseration sequences are fenetics elements that can move from one location on a host DNA molecile to another by transposition. Transposition can be either replicative or conseracrive. transposons often carry genes encodin antibiotic resistance and can be used as biological mutagens
the clustered regulatory interspaced short palindromic repeat (CRISPR) sustem is an RNA based mechanism of protecting the prokaryotic genome from invading DNA resulting from infection and conjugation. if the small RNA moleciles resilting from the spaver regions of the CRISPR region bind to the incoming complemetary DNA, Cas proteins destroy the nucleic acid dupluex
restriction enzymes recognize specific short sequences of DNA and make cuts in tbe DNA. the porductws made can be shown using gel electrophoreisis
complementary nucleic acid seuqences may be detected by hybridization. proves composed of single stranded DNA or RNA and labeled with radioactive/fluorescent dye are hybridized to target DNA/RNA sequences
PCR polymerase chain reaction; amplifying DNA in vitro and employs heat stable DNA polymerase. heat is used to denature. anneal primers. enlongate dna- doubles DNA each time
Molecular cloning is used to isolate specific gene. use a plamid or virus as a cloning vector. resitriction enzymes and DNA ligase are used in vitro to produce a chimeric dna moleuel conposed of DNA from two or more sourecs. once introduced into a suitable host the cloned dna can be produced in largge amounts under the control of the cloning vector. identification of the cloned genes is performed by a range of molecular techniques
symtheic dna molecules of desired sequence can be made in vitro and used to construct a mutated gene directly or to change specific base pairs within a gene by sire directed mutagenesis. also denes can be distrupted by inserting dna fragments called cassettes into them, generating knockout mutants
reporter genes are genes whose products such as B gal pr GFP are easy to assay or detect. They are used to simplify and increase the speed of genetic analysis. In gene fusions, segments from 2 different genes one of which is usually a reporter gene are spliced together
plasmids are good cloning vectors because theya re easy to isolate and purify and are often able to muliply. antibiotic resitsance genes on the plasmid are used to select bacterial cells containing plasmid and color scrrening ssytems are used to idenitfy colonies containing cloned dna
first human protein made coommerically using engineered bacteria was human insulin. recombinant bovine somatotrpohin is widely used in USA to increase milk yield in dairy cows
genetic engineering can make plants resistant to disease and improve product quality
many recombinant vaccines have been produced or are under development. these inclide live recombinant, vector, and subunit vacccines
genes for useful products may be cloned directly from DNA or RNA in environmental smaples wotjhout first isolating the oragnisms that carry them
Northern v southern blot
N: RNA is target, DNA or RNA is probe
S: DNA is target, DNA or RNA is probe
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