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)