AP Bio - Chapter 19,20,27
Organismal cloning produces one or more organisms genetically identical to the
"parent" that donated the single cell
Most prokaryotic cells are - µm,
0.5-5
Prokaryotes can divide every
1-3 hours
Prokaryotic cells are much smaller than the - µm of many eukaryotic cells
10-100
Genetic markers called SNPs (single nucleotide polymorphisms) occur on average every
100-300 base pairs
Human intestines are home to about - species of bacteria
500-1,000
Symbiosis
A close relationship between two species that benefits at least one of the species. a larger host and smaller symbiont
In bacteria, the DNA transfer is one way
A donor cell attaches to a recipient by a pilus, pulls it closer, and transfers DNA
prophage
A phage genome that has been inserted into a specific site on the bacterial chromosome. integrated viral DNA in lysogenic cycle
virulent phage
A phage that reproduces only by a lytic cycle.
F factor
A piece of DNA that confers the ability form a sex pili A piece of DNA that is required for the production of pili
capsule
A polysaccharide or protein layer that covers many prokaryotes
transformation
A prokaryotic cell can take up and incorporate foreign DNA from the surrounding environment in this process
genomic library
A set of thousands of DNA segments from a genome, each carried by a plasmid, phage, or other cloning vector.
Southern blotting
A technique that enables specific nucleotide sequences to be detected in a sample of DNA. It involves gel electrophoresis of DNA molecules and their transfer to a membrane (blotting), followed by nucleic acid hybridization with a labeled probe.
electroporation
A technique to introduce recombinant DNA into cells by applying a brief electrical pulse to a solution containing the cells. The pulse creates temporary holes in the cells' plasma membrane, through which DNA can enter.
Endospores
A thick-walled protective spore that forms inside a bacterial cell and resists harsh conditions.
bacteriophages
A virus that infects bacteria; also called a phage.' such as Escherichia coli
Gram-positive bacteria include
Actinomycetes, which decompose soil Bacillus anthracis, the cause of anthrax Clostridium botulinum, the cause of botulism Some Staphylococcus and Streptococcus, which can be pathogenic Mycoplasms, the smallest known cells
Retroviruses
An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.
Pili
Appendages that allow bacteria to attach to each other and to transfer DNA longer than fimbriae and allow prokaryotes to exchange DNA
extremophiles
Archaea that live in extreme environments.
Biofilms
Colonies of bacteria that adhere together and adhere to environmental surfaces. metabolic cooperation occurs in surface-coating colonies
DNA cloning allows researchers to
Compare genes and alleles between individuals Locate gene expression in a body Determine the role of a gene in an organism
Viral genomes may consist of either
Double- or single-stranded DNA, or Double- or single-stranded RNA
Changes in the expression of a gene during embryonic development can be tested using
Northern blotting Reverse transcriptase-polymerase chain reaction Both methods are used to compare mRNA from different developmental stages
Prokaryotic metabolism varies with respect to
O2
Obligate aerobes require
O2 for cellular respiration
anearobic respiration
Occurs in the absence of oxygen
decomposers
Organisms that break down the dead remains of other organisms Chemoheterotrophic prokaryotes function as this
Autotrophs
Organisms that make their own food
SNPs can be detected by
PCR
Scientists can diagnose many human genetic disorders using - and -
PCR and sequence-specific primers, then sequencing the amplified product to look for the disease-causing mutation
temperate phages
Phages that use both the lytic and lysogenic cycles
gel electrophoresis
Procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel
In nitrogen fixation,
Process of converting nitrogen gas into ammonia] some prokaryotes convert atmospheric nitrogen (N2) to ammonia (NH3)
Genetic profiles can be analyzed using RFLP analysis by
Southern blotting
7 steps are required to clone the hummingbird β-globin gene in a bacterial plasmid
The hummingbird genomic DNA and a bacterial plasmid are isolated Both are cut with the same restriction enzyme The fragments are mixed, and DNA ligase is added to bond the fragment sticky ends Some recombinant plasmids now contain hummingbird DNA The DNA mixture is added to bacteria that have been genetically engineered to accept it The bacteria are plated on a type of agar that selects for the bacteria with recombinant plasmids This results in the cloning of many hummingbird DNA fragments, including the β-globin gene
Gene therapy
The insertion of working copies of a gene into the cells of a person with a genetic disorder in an attempt to correct the disorder
key to three step cycle is
The key to PCR is an unusual, heat-stable DNA polymerase called Taq polymerase.
F plasmid
The plasmid form of the F factor. function as DNA donors during conjugation
nucleic acid hybridization
The process of base pairing between a gene and a complementary sequence on another nucleic acid molecule.
horizontal gene transfer
The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps fusions of different organisms.
provirus
The viral DNA that is integrated into the host genome
3 key features of prokaryotic reproduction:
They are small They reproduce by binary fission They have short generation times
Gram stain
Used to classify prokaryotes based on cell wall composition. Important for antibiotics; some antibiotics work on one but not the other.
HIV is a retrovirus, that causes
Uses RNA as genetic code instead of DNA AIDS
To overcome differences in promoters and other DNA control sequences, scientists usually employ an expression vector,
a cloning vector that contains a highly active bacterial promoter
Mimivirus
a double-stranded DNA virus, the largest virus yet discovered, is the size of a small bacterium
Each virus has a host range
a limited number of host cells that it can infect
An example of DNA technology is the microarray,
a measurement of gene expression of thousands of different genes
dideoxyribonucleotides
a nucleotide used in DNA sequenceing that is missing the 3'-OH group. It stops any further growth of the DNA strand if inserted.
In the late 1800s, researchers hypothesized that
a particle smaller than bacteria caused the disease
Cloned genes are useful for making copies of - and -
a particular gene and producing a protein product
stem cell
a relatively unspecialized cell that can reproduce itself indefinitely and differentiate into specialized cells of one or more types
heterocysts
a specialized cell that engages in nitrogen fixation in some filamentous cyanobacteria
iPS cells
a type of pluripotent stem cell that can be generated directly from adult cells induced pluripotent cells
Prokaryotes thrive almost everywhere, including places too
acidic, salty, cold, or hot for most other organisms
Scientists hypothesize that mitochondria evolved from
aerobic alpha proteobacteria through endosymbiosis
Nitrogen is essential for the production of
amino acids and nucleic acids
restriction enzymes
Enzyme that cuts DNA at a specific sequence of nucleotides
Molecular systematics led to the splitting of prokaryotes into
bacteria and archaea
Prokaryotes are divided into two domains:
bacteria and archaea
Archaea share certain traits with ______ and other traits with ______
bacteria, eukaryotes
recombinant plasmid is inserted into a
bacterial cell
Prokaryotes reproduce quickly by
binary fission
mutualism
both organisms benefit
Synthetic double-stranded RNA molecules matching the sequence of a particular gene are used to
break down or block the gene's mRNA
Three step cycle of PCR
brings about a chain reaction that produces an exponentially growing population of identical DNA molecules
parasitism
an organism called a parasite harms but does not kill its host
The broadest variety of RNA genomes is found in viruses that infect
animals
Gram-negative bacteria are more likely to be
antibiotic resistant
Viral infections cannot be treated by
antibiotics
Prions
are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals
Viroids
are small circular RNA molecules that infect plants and disrupt their growth
Fimbriae
attachment structures on the surface of some prokaryotes
Prokaryotes can also "immobilize" or decrease the
availability of nutrients
Reverse transcriptase is added to mRNA to make
cDNA, which serves as a template for PCR amplification of the gene of interest The products are run on a gel and the mRNA of interest is identifiedIn
Viruses are obligate intracellular parasites, which means they
can replicate only within a host cell
Capsids are built from protein subunits called
capsomeres
A cloning vector is a DNA molecule that can
carry foreign DNA into a host cell and replicate there
R plasmids
carry genes for antibiotic resistance
Viruses are not
cells
Eukaryote cell walls are made of - or -
cellulose, chitin
The ecological communities of hydrothermal vents depend on
chemoautotrophic bacteria for energy
Most of the genome consists of a - chromosome
circular
A complementary DNA (cDNA) library is made by
cloning DNA made in vitro by reverse transcription of all the mRNA produced by a particular cell
Reproduction in the bacterial cell results in
cloning of the plasmid including the foreign DNA This results in the production of multiple copies of a single gene
In gene cloning, the original plasmid is called a
cloning vector
A genomic library that is made using bacteriophages is stored as a
collection of phage clones
Northern blotting
combines gel electrophoresis of mRNA followed by hybridization with a probe on a membrane
Ti plasmid is the most
commonly used vector for introducing new genes into plant cells
Northern blotting and Reverse transcriptase-polymerase chain reactio, both methods are used to
compare mRNA from different developmental stages
DNA microarray assays
compare patterns of gene expression in different tissues, at different times, or under different conditions
A probe can be synthesized that is - to the gene of interest
complementary
Sticky ends can bond with
complementary sticky ends of other fragments
Bacteriophages have the most - capsids found among viruses
complex
Prokaryotic cells usually lack
complex compartmentalization
Prions propagate by
converting normal proteins into the prion version
In lysogenic cycle every time the host divides, it
copies the phage DNA and passes the copies to daughter cells
In 1935, Wendell Stanley confirmed this hypothesis by
crystallizing the infectious particle, now known as tobacco mosaic virus (TMV)
lytic cycle is a phage replicative cycle that
culminates in the death of the host cell
Plant chloroplasts likely evolved from
cyanobacteria by the process of endosymbiosis
Why can people use antibiotics
differences between prokaryotes and eukaryotes in DNA replication, transcription, and translation
Restriction fragment analysis can be used to compare two
different DNA molecules, such as two alleles for a gene, if the nucleotide difference alters a restriction site
Flagella of bacteria, archaea, and eukaryotes are composed of
different proteins and likely evolved independently
One way to determine function is to
disable the gene and observe the consequences
SNPs may be associated with a
disease-causing mutation
Genetic recombination, the combining of DNA from two sources, contributes to
diversity
A cell with the F factor built into its chromosomes functions as a
donor during conjugation
Phages have an - capsid that encloses their DNA
elongated capsid head
Stem cells isolated from early embryos at the blastocyst stage are called
embryonic stem (ES) cells; these are able to differentiate into all cell types
Horizontal transmission,
entering through damaged cell walls
The virus makes use of host
enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules
Molecular biologists can avoid eukaryote-bacterial incompatibility issues by using
eukaryotic cells, such as yeasts, as hosts for cloning and expressing genes
Many species are closely associated with
eukaryotic hosts
Their short generation time allows prokaryotes to
evolve quickly
Pathogenic prokaryotes typically cause disease by releasing
exotoxins or endotoxins
Obligate anaerobes are poisoned by O2 and use
fermentation or anaerobic respiration
Most motile bacteria propel themselves by
flagella scattered about the surface or concentrated at one or both ends
Pax-6 is a gene that directs formation of a vertebrate eye; the same gene in flies directs the
formation of an insect eye (which is quite different from the vertebrate eye)
Prokaryotes cause about - of all human diseases
half
Vaccines
harmless derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the harmful pathogen
SNPs may also be correlated with increased risks for conditions such as
heart disease or certain types of cancer
A three-step cycle
heating, cooling, and replication
Plant viruses spread disease in two major modes
horizontal transmission and vertical transmission
One benefit of DNA technology is identification of
human genes in which mutation plays a role in genetic diseases
Diseases caused by viral infections affect
humans, agricultural crops, and livestock worldwide
Viruses may damage or kill cells by causing the release of - from lysosomes
hydrolytic enzymes
Each type of ddNTP is tagged with a distinct fluorescent label that
identifies the nucleotide at the end of each DNA fragment The DNA sequence can be read from the resulting spectrogram
In situ hybridization uses fluorescent dyes attached to probes to
identify the location of specific mRNAs in place in the intact organism
Experiments using prokaryotes have led to
important advances in DNA technology
For the lysogenic cycle he viral DNA molecule is
incorporated into the host cell's chromosome
prions
infectious protein particles that do not have a genome infect animals
Vertical transmission,
inheriting the virus from a parent
A protein tail piece attaches the phage to the host and
injects the phage DNA inside
Prokaryotes can be categorized by how they obtain energy and carbon
into 4 trophs types
Specific DNA fragments can be identified by Southern blotting, using
labeled probes that hybridize to the DNA immobilized on a "blot" of gel
bacterial artificial chromosome (BAC) is a
large plasmid that has been trimmed down and can carry a large DNA insert
Prokaryotes often form symbiotic relationships with
larger organisms
The prokaryotic genome has - DNA than the eukaryotic genome
less
Reverse transcriptase-polymerase chain reaction (RT-PCR) is quicker and more sensitive because it requires
less mRNA than Northern blotting
Gram-negative bacteria have
less peptidoglycan and an outer membrane that can be toxic
Viruses lead "a kind of borrowed life" between
life-forms and chemicals
Extreme halophiles
live in highly saline environments, such as the Great Salt Lake and the Dead Sea
Methanogens
live in swamps and marshes and produce methane as a waste product
Mutation rates during binary fission are
low but because of rapid reproduction, mutations can accumulate rapidly in a population
An environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the
lytic mode
The RNA molecules function both as - and -
mRNA for synthesis of viral proteins and as genomes for new virus particles released from the cell
Nucleic acid probes can hybridize with
mRNAs transcribed from a gene
Transgenic animals are
made by introducing genes from one species into the genome of another animal
An important feature of nearly all prokaryotic cells is their cell wall, which
maintains cell shape, protects the cell, and prevents it from bursting in a hypotonic environment
Once a viral genome has entered a cell, the cell begins to
manufacture viral proteins
Many viruses that infect animals have a
membranous envelope
Some viruses have - that help them infect hosts
membranous envelopes
Some prokaryotes do have specialized membranes that perform
metabolic functions usually infoldings of the plasma membrane
Genetic engineering can be used to modify the
metabolism of microorganisms
scientists can inject DNA into cells using - instead of electroporation
microscopically thin needles
When the mutated gene is returned to the cell, the normal gene's function
might be determined by examining the mutant's phenotype
Plasmids, transposons, and viruses are all
mobile genetic elements
gel electrophoresis uses a gel as a
molecular sieve to separate nucleic acids or proteins by size, electrical charge, and other properties a current is applied that causes charged molecules to move through the gel molecules are sorted into "bands" by their size
The use of polymerase chain reaction (PCR) has allowed for
more rapid sequencing of prokaryote genomes
Bacterial flagella are composed of 3 parts
motor, hook, and filament
Transduction is the
movement of genes between bacteria by bacteriophages
Chemotaxis is the
movement toward or away from a chemical stimulus
Using in vitro mutagenesis,
mutations are introduced into a cloned gene, altering or destroying its function
Once inside the cell, the DNA is incorporated into the cell's DNA by
natural genetic recombination
Bacterial cell walls contain peptidoglycan, a
network of sugar polymers cross-linked by polypeptides
lytic cycle produces
new phages and lyses (breaks open) the host's cell wall, releasing the progeny viruses
Prokaryotes can sometimes increase the availability of
nitrogen, phosphorus, and potassium for plant growth
he adult body also has stem cells, which replace
nonreproducing specialized cells
Other viral membranes form from the host's
nuclear envelope and are then replaced by an envelope made from Golgi apparatus membrane
A virus is a very small infectious particle consisting of
nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope
A clone carrying the gene of interest can be identified with a
nucleic acid probe having a sequence complementary to the gene
Depending on its type of - a virus is called a DNA virus or an RNA virus
nucleic acid,
The chromosome is not surrounded by a membrane; it is located in the -region
nucleoid
recombinant DNA
nucleotide sequences from two different sources, often two species, are combined in vitro into the same DNA molecule
Chemotrophs
obtain energy from chemicals
Phototrophs
obtain energy from light
commensalism
one organism benefits and the other is unaffected
totipotent cell is
one that can generate a complete new organism
Heterotrophs
organisms that cannot make their own food and must feed on other organisms for energy and nutrients
pathogens
parasites that cause disease
Chlamydias
parasites that live within animal cells; chlamydia trachomatis causes blindness and nongonococcal urethritis by sexual transmission
Archaea contain polysaccharides and proteins but lack -
peptidoglycan
Many antibiotics target
peptidoglycan and damage bacterial cell walls
Unlike a prophage, a provirus remains a
permanent resident of the host cell
gram-negative bacteria include 3 troph types
photoautotrophs, chemoautotrophs, and heterotrophs Some are anaerobic, and others aerobic
SNP shared by people affected with a disorder but not among unaffected people may
pinpoint the location of the disease-causing gene
Some viral envelopes are formed from the host cell's - as the viral capsids exit
plasma membrane
Foreign DNA is inserted into a
plasmid
Candidates for the source of viral genomes are
plasmids, circular DNA in bacteria and yeasts, and transposons, small mobile DNA segments
Variations in DNA sequence are called
polymorphisms
polymerase chain reaction, PCR, can
produce many copies of a specific target segment of DNA
hybridize
produce offspring between genetically different strains
After a gene has been cloned, its protein product can be
produced in larger amounts for research
Bacteria include the vast majority of
prokaryotes
Prokaryotes are so important that if they were to disappear the
prospects for any other life surviving would be dim
Host cells in culture can be engineered to secrete a
protein as it is made, simplifying the task of purifying it This is useful for the production of insulin, human growth hormones, and vaccines
Identification of mRNA at a particular developmental stage suggests
protein function at that stage
cloned genes can be expressed as
protein in either bacterial or eukaryotic cells
A capsid is the
protein shell that encloses the viral genome
Many of the flagella's proteins are modified versions of
proteins that perform other tasks in bacteria
High diversity from mutations allows for
rapid evolution
Prokaryotes play a major role in the
recycling of chemical elements between the living and nonliving components of ecosystems
Endotoxins
released only when bacteria die and their cell walls break down
lysogenic cycle
replicates the phage genome without destroying the host
A restriction enzyme usually makes many cuts, yielding
restriction fragments
Bacterial restriction enzymes cut DNA molecules at specific DNA sequences
restriction sites
Bacteria have defenses against phages, including - enzymes
restriction, that recognize and cut up certain phage DNA
Retroviruses use
reverse transcriptase to copy their RNA genome into DNA
Many epigenetic changes, such as acetylation of histones or methylation of DNA, must be
reversed in the nucleus from a donor animal in order for genes to be expressed or repressed appropriately for early stages of development
DNA ligase is an enzyme that
seals the bonds between restriction fragments
Exotoxins
secreted and cause disease even if the prokaryotes that produce them are not present
short tandem repeats (STRs)
sections of a chromosome in which DNA sequences are repeated variations in the number of repeats of specific DNA sequences which are PCR and gel electrophoresis are used to amplify and then identify STRs of different lengths
Viral nucleic acid molecules and capsomeres spontaneously
self-assemble into new viruses
Gram-positive bacteria have
simpler walls with a large amount of peptidoglycan
Gene therapy holds great potential for treating disorders traceable to a
single defective gene
Plasmids
small circular DNA molecules that replicate separately from the bacterial chromosome
plasmids
small circular DNA molecules that replicate separately from the bacterial chromosome
viroids
small circular RNA molecules that infect plants and disrupt their growth
The drug imatinib is a
small molecule that inhibits overexpression of a specific leukemia-causing receptor
In most nuclear transplantation studies, only a
small percentage of cloned embryos have developed normally to birth, and many cloned animals exhibit defects
In restriction fragment analysis, DNA fragments produced by restriction enzyme digestion of a DNA molecule are
sorted by gel electrophoresis
Viral glycoproteins on the envelope bind to
specific receptor molecules on the surface of a host cell
Vectors are used for delivery of genes into
specific types of cells
The three most common shapes of prokaryotic cells
spheres (cocci), rods (bacilli), and spirals
helical heterotrophs
spirochetes Some are parasites, including Treponema pallidum, which causes syphilis, and Borrelia burgdorferi, which causes Lyme disease
More than 2,000 types of viral diseases of plants are known and cause
spots on leaves and fruits, stunted growth, and damaged flowers or roots
The most useful restriction enzymes cut DNA in a staggered way, producing fragments with
sticky ends
Methanogens are
strict anaerobes and are poisoned by O2
A cDNA library represents only part of the genome—only the
subset of genes transcribed into mRNA in the original cells
viral envelopes
surround the capsids of influenza viruses and many other viruses found in animals
1997, Scottish researchers announced the birth of Dolly her death in 2003 made scientists speculate
that her cells were not as healthy as those of a normal sheep, possibly reflecting incomplete reprogramming of the original transplanted nucleus
In a heterogeneous environment, many bacteria exhibit taxis
the ability to move toward or away from a stimulus
The DNA probe can be used to screen a large number of clones simultaneously for the gene of interest, once identified,
the clone carrying the gene of interest can be cultured
Relatively short DNA fragments can be sequenced by
the dideoxy chain termination method, the first automated method to be employed
Methods for making recombinant DNA are central to genetic engineering
the direct manipulation of genes for practical purposes
Phages have two reproductive mechanisms:
the lytic cycle and the lysogenic cycle
biotechnology
the manipulation of organisms or their genetic components to make useful products
In nuclear transplantation, the nucleus of an unfertilized egg cell or zygote is replaced with
the nucleus of a differentiated cell
Prokaryotes are the principal agents in bioremediation
the use of organisms to remove pollutants from the environment
Extreme thermophiles
thrive in very hot environments (archaea)
Some viruses have molecular components such as envelope proteins that are
toxic
Some viruses cause infected cells to produce
toxins that lead to disease symptoms
The F factor is - during conjugation
transferable
Prokaryotic DNA from different individuals can be brought together by
transformation, transduction, and conjugation
The recipient becomes a recombinant bacterium, with DNA from
two different cells
Most prokaryotes are
unicellular, although some species form colonies
genomic library is made
using bacteria is the collection of recombinant vector clones produced by cloning DNA fragments from an entire genome
Gene cloning involves
using bacteria to make multiple copies of a gene
Antiviral drugs can help to treat, though not cure,
viral infections
Researchers can transform skin cells into ES cells by using
viruses to introduce stem cell master regulatory genes
exaptation,
where existing structures take on new functions through descent with modification
Conjugation is the process
where genetic material is transferred between prokaryotic cells
Probes can be used to identify
where or when a gene is transcribed in an organism
One experimental approach for testing genomic equivalence is to
whether a differentiated cell can generate a whole organism
Some prokaryotes have fimbriae
which allow them to stick to their substrate or other individuals in a colony
Many prokaryotes form metabolically inactive endospores
which can remain viable in harsh conditions for centuries
Facultative anaerobes can survive
with or without O2
cultured mammalian or insect cells may be used to express and study proteins if
yeasts may not possess the proteins required to modify expressed mammalian proteins properly
To work directly with specific genes, scientists prepare well-defined segments of DNA in identical copies, a process
DNA cloning
BACs are another type of vector used in
DNA library construction
There are some differences between prokaryotes and eukaryotes in 3 process
DNA replication, transcription, and translation
The host's RNA polymerase transcribes the proviral DNA into
RNA molecules
Prokaryotes have considerable genetic variation, three factors contribute to this genetic diversity
Rapid reproduction Mutation Genetic recombination
Sequence changes that alter restriction sites are called
RFLPs (restriction fragment length polymorphisms)
Most plant viruses have an - genome
RNA
Gene expression can also be silenced using
RNA interference (RNAi)