Term
| For a molecule to serve as the genetic material, it must be able to: |
|
Definition
replicate
store information
express information
allow variation by mutation |
|
|
Term
| Central dogma of genetics |
|
Definition
DNA to RNA to protein
DNA->(Transcription)->RNA->(translation)->Protein |
|
|
Term
| Griffith's Mouse Experiment |
|
Definition
Was the first evidence that DNA was genetic material.
He had two different strains of bacteria, a virulent strain (IIIS) and a anvirulent strain (IIR). The virulent strain when injected into the mouse killed it and the avirulent strain would not affect the mouse. When he heat killed the IIIS strain, the mouse also lived. When he mixed the heat killed IIIS strain and the IIR strain, the mouse died. After observations, he discovered that the IIIS strain somehow recovered. |
|
|
Term
| Avery, MacLeod, and McCarty's experiment |
|
Definition
Showed that the transforming principle was DNA.
In their experiment, they took some IIIS cells, heat killed it and extracted the carbohydrates, lipids, and proteins. They then took this filtrate and added it to IIR cells and a particular enzyme that either impeded RNA, DNA, or protein. The only resulting tube that only had IIR cells in it (meaning that the genetic information in the IIIS cells couldn't be recovered) was the filtrate that was mixed with deoxyribonuclease. |
|
|
Term
| Hershey and Chase experiment |
|
Definition
Demonstrated that DNA and not protein enters the bacterial cell during bacteriophage infection.
They did this by marking the different material of the phages. The DNA portion of one phage was marked blue and the protein portion of another was marked green. After infection, they found that the phages no longer had the blue labeling as the blue was now inside the bacteria, and that the phage with the green labeling remained green and the bacteria remained unlabeled. |
|
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Term
|
Definition
| deliberately putting viral DNA into bacterial cells |
|
|
Term
| Indirect evidence in support of DNA being the genetic material |
|
Definition
DNA is found only where the primary genetic function occurs
UV light causes genetic mutations at 260 nm and this is the wavelength that DNA and RNA absorb the most. Protein absorbs at 280 nm and no mutations occur at this wavelength |
|
|
Term
| Direct Evidence of DNA being the genetic material |
|
Definition
| Recombinant DNA technology. The presence of the eukaryotic gene product in bacteria containing the eukaryotic gene provides direct evidence that this DNA is present and functional in the bacterial cell. |
|
|
Term
| The building blocks of DNA |
|
Definition
|
|
Term
|
Definition
a nitrogenous base
a pentose sugar
a phosphate group - located on the 5th carbon of the ring |
|
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Term
|
Definition
| Adenine and guanine. Have two rings |
|
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Term
|
Definition
| Cytosine, thymine, and uracil. Have one ring |
|
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Term
|
Definition
| contains the nitrogenous base and the pentose sugar, NOT the phosphate group |
|
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Term
|
Definition
| Links the phosphate group on the C5 position and the OH group on the C3 position of another nucleotide |
|
|
Term
| How many phosphate groups can a nucleotide have? |
|
Definition
Up to 3
NMPs, NDPs, and NTPs |
|
|
Term
|
Definition
| The amount of A is proportional to T and the amount of G is proportional to C but C+G doesn't necessarily equal A+T |
|
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Term
|
Definition
| Was able to show that DNA had a helical structure. Done by the chick that I can't remember her name :-( |
|
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Term
|
Definition
| Proposed DNA is a right-handed double helix in which two strands are antiparallel. Strands are connected by A-T and G-C base pairing and there are 10 bp's per helix turn |
|
|
Term
| A-T base pair, # of hydrogen bonds |
|
Definition
|
|
Term
| G-C base pair, # of hydrogen bonds |
|
Definition
|
|
Term
|
Definition
| the biologically signifanct form of DNA |
|
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Term
|
Definition
B-DNA
C-DNA, D-DNA, E-DNA
Z-DNA |
|
|
Term
|
Definition
| right handed forms of DNA that are less compact than D-DNA |
|
|
Term
|
Definition
| forms a left-handed double helix |
|
|
Term
|
Definition
| contains the sugar ribose and has uracil instead of thymine |
|
|
Term
|
Definition
messenger RNA - are the template for protein synthesis
ribosomal RNA - components of ribosomes for protein synthesis
transfer RNA - carry amino acids for protein synthesis |
|
|
Term
| Sedimentation equilibrium centrifugation |
|
Definition
| separates by density gradient. |
|
|
Term
| Sedimentation velocity centrifugation |
|
Definition
| measures the velocity of sedimentation in Svedberg coefficient units. |
|
|
Term
|
Definition
| increase in UV absorption |
|
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Term
|
Definition
| DNA strands (or DNA and RNA strands) can be renatured to each other. |
|
|
Term
| Fluorescent in situ hybridization (FISH) |
|
Definition
| is used to identifying the chromosomal location of a DNA of interest |
|
|
Term
|
Definition
| provides information about the size and complexity of genomic DNA from an organism |
|
|
Term
| Nucleic acid electrophoresis |
|
Definition
| separates DNA and RNA fragments by size such that smaller fragments migrate through a gel at a faster rate than large fragments |
|
|
Term
| Three mods of DNA replication |
|
Definition
conservative
semiconservative
dispersive |
|
|
Term
| Meselson-Stahl Experiment |
|
Definition
| Demonstrated that DNA is semiconservative - each new DNA molecule consists of one old strand and one newly synthesized strand |
|
|
Term
| DNA replication begins at the |
|
Definition
| origin of replication and is bidirectional |
|
|
Term
|
Definition
| the length of DNA that is replicated following one initiation event at a single origin. |
|
|
Term
| Requirements for Replication |
|
Definition
DNA template
enzymes
dATP, dTTP, dGTP, dCTP |
|
|
Term
|
Definition
catalyzes DNA synthesis and requires a DNA template and all four dNTPs. Elongates an existing DNA strand but can't initiate DNA synthesis.
I, II, and III have 3' to 5; exonuclease activity but only DNA polymerase I demonstrates 5' to 3' exonuclease activity |
|
|
Term
| Chain elongation direction |
|
Definition
|
|
Term
|
Definition
the enzyme responsible for the 5' to 3' polymerization essential in vivo.
Its 3' to 5' exonuclease activity allows proofreading.
Has 10 subunits |
|
|
Term
|
Definition
| responsible for removing the primer and the synthesis that fills gaps produced during synthesis |
|
|
Term
|
Definition
binds to the origin of replication and is responsible for the initial steps in unwinding the helix.
DnaB and DnaC further opens and destabilizes the helix. |
|
|
Term
| Single-stranded binding proteins (SSBPs) |
|
Definition
| stabilize the open conformation. |
|
|
Term
|
Definition
| Proteins that break hydrogen bonds and denature the double helix |
|
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Term
|
Definition
| relieves supercoiling. A member of the topoisomerases |
|
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Term
|
Definition
| Synthesizes an RNA primer that provides the fee 3'hydroxyl required by DNA pol III. DNA is then added after the primer |
|
|
Term
|
Definition
| serves as a template for continuous DNA synthesis |
|
|
Term
|
Definition
| undergoes discontinuous DNA synthesis. Is synthesized as Okazaki fragments. |
|
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Term
|
Definition
| joins the Okazaki fragments of the lagging strand after the primers are removed |
|
|
Term
|
Definition
| prevents the core enzyme from falling off the template during DNA synthesis. |
|
|
Term
| DNA synthesis at a single replication fork involves |
|
Definition
DNA pol III
SSBPs
DNA gyrase
DNA helicase
RNA primers |
|
|
Term
| temperature-sensitive mutation |
|
Definition
an example of a conditional mutation.
It may not be expressed at a particular permissive temperature, but when mutant cells are grown at a restrictive temperature, the mutant phenotype is expressed and can be studied. |
|
|
Term
| the major forms of the enzyme involved in initiation and elongation. |
|
Definition
|
|
Term
|
Definition
| a term that reflects the length of DNA that is synthesized by an enzyme before it dissociates from the template. |
|
|
Term
|
Definition
One of the major forms of the enzyme involved in initiation and elongation.
functions in synthesis of the RNA primers during initiation on the leading and lagging strands. |
|
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Term
|
Definition
| consist of long stretches of short repeating sequences and preserve the integrity and stability of chromosomes. |
|
|
Term
|
Definition
| directs synthesis of the telomere repeat sequence to fill the gap left bind by the last RNA primer removed |
|
|
Term
|
Definition
|
|
Term
| General or homologous recombinatoin |
|
Definition
| Genetic exchange at equivalent positions along two chromosomes with substantial DNA sequence homology |
|
|
Term
|
Definition
| In E. coli, promotes the exchange of reciprocal single-stranded DNA molecules |
|
|
Term
|
Definition
| a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones (H2A, H2B, H3, and H4) |
|
|
Term
|
Definition
| compacted double-stranded DNA for bacteria. Associated with HU and HI DNA-binding proteins |
|
|
Term
|
Definition
| cut one or both DNA strands and wind or unwind the helix before resealing the ends. |
|
|
Term
|
Definition
are very large and can be visualized by light microscopy.
have distinctive banding patterns
represent paired homologs
are composed of many DNA strands |
|
|
Term
|
Definition
| Region where DNA has uncoiled and are visible manifestations of a high level of gene activity (transcription). Found in polytene chromosomes |
|
|
Term
|
Definition
| are large and have extensive DNA looping. They are found in oocytes in the diplotene stage of meiosis. |
|
|
Term
|
Definition
| A nucleoprotein structure containing compacted eukaryotic chromosomes |
|
|
Term
|
Definition
| are important for histone modifications such as acetylation, methylation, and phosphorylation |
|
|
Term
|
Definition
|
|
Term
|
Definition
| remains condensed and is inactive |
|
|
Term
|
Definition
| only the centromeres are stained |
|
|
Term
|
Definition
| due to differential staining along the length of each chromosome |
|
|
Term
|
Definition
| highly repetitive and consists of short repeated sequences |
|
|
Term
| Moderately repetitive DNA includes |
|
Definition
variable number tandem repeats (VNTRs)
minisatellites
microsatellites |
|
|
Term
| Short interspersed elements (SINES) and long interspersed elements (LINES) are |
|
Definition
| dispersed throughout the genome rather than tandemly repeated, and constitute over 1/3 of the human genome. Are referred to as retrotransposons |
|
|
Term
|
Definition
| single-copy noncoding regions of DNA |
|
|
Term
|
Definition
| Nucleosome core + one molecule of histone H1. |
|
|
Term
|
Definition
| The conversion of amino acids into polypeptide chains |
|
|
Term
| The translation process requires 4 things: |
|
Definition
amino acids
mRNA
ribosomes
tRNA |
|
|
Term
|
Definition
consist of ribosomal proteins and rRNAs
Have a large and small subunit |
|
|
Term
|
Definition
| serve as adaptor molecules to adapt triplet codons in mRNA to the correct amino acid |
|
|
Term
| Posttranscriptionally modified |
|
Definition
|
|
Term
| What does the anticodon in tRNA bind to? |
|
Definition
|
|
Term
| Where is the amino acid bound to in tRNA? |
|
Definition
| the CCA sequence at the 3' end |
|
|
Term
| Aminoacyl tRNA synthetase |
|
Definition
| activates tRNA with the appropriate amino acid. The tRNA is considered "charged" now |
|
|
Term
|
Definition
initiation
elongation
termination |
|
|
Term
| Initiation of translation |
|
Definition
small and large ribosomal subunits
GTP
charged initiator tRNA
initiation factors IF I, II, and III |
|
|
Term
|
Definition
mRNA binds to small subunit along with IF1, 2, and 3 which forms an initiation complex
initiator tRNA binds to mRNA codon at the p site, IF 3 is released
Large subunit binds to the complex, IF1 and IF2 released, EF-Tu + GDP facilitate in helping entry into A site |
|
|
Term
|
Definition
|
|
Term
|
Definition
| both ribosomal subunits assembled with the mRNA to form the P and A site |
|
|
Term
| Steps of elongation for translation |
|
Definition
After the initiator tRNA is bound to the P site, a second tRNA comes in and binds to the A site (facilitated by EF-Tu + GDP).
A peptide bond forms between the amino acids held by the two tRNAs (facilitated by peptidyl transferase)
which removes the acid from the tRNA in the P site uncharging it and adding it to the tRNA in the A site
The uncharged tRNA goes to the E site where it leaves (facilitated by EF-G + GDP)
The mRNA shifts a codon to the left making the tRNA move from A to P
This process continues until the stop codon on the mRNA is reached (UAG, UAA, UGA) |
|
|
Term
|
Definition
|
|
Term
| GTP-dependent release factors |
|
Definition
| cleave the polypeptide chain from the tRNA and release it from the complex during termination |
|
|
Term
| Steps to termination or translation |
|
Definition
| tRNA and polypeptide chain released GTP-dependent termination factors are activated, the two subunits of RNA separate and the polypeptide folds into protein |
|
|
Term
|
Definition
| mRNAs with several ribosomes translating at once |
|
|
Term
| Crystalloraphic analysis has helped us learn about rib0somes by looking at a prokaryotic ribosome |
|
Definition
|
|
Term
| Translation is more complex in eukaryotes because |
|
Definition
ribosomes are larger
transcription and translation are spatially and temporally separated
requires more factors |
|
|
Term
|
Definition
identifies the correct iniation tRNA
5' -ACCAUGG-3' |
|
|
Term
| Alkatonuria and phenylketonuria result from |
|
Definition
| mutations that lead to metabolic blocks. This gave evidence that proteins are important to heredity |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| One-Gene One-Enzyme hypothesis |
|
Definition
|
|
Term
| Beadle and Tatum neurospora experiment |
|
Definition
Had some spores that they irradiated to increase mutations and grew both the normal and mutant sports on complete and minimal medium.
In the first part of the experiment, they found that the normal spores grew on both mediums and that the mutated spore grew only in complete medium.
In the second part of the experiment, they took the spores and grew them on medium with different supplements and subsequently grew them on more singular mediums such as different kinds of amino acids.
When they found growth, they were able to determine that the supplement was the molecule that the strain couldn't synthesize |
|
|
Term
| Because not all proteins are enzymes, the one gene one enzyme hypothesis changed to: |
|
Definition
| one gene one protein hypothesis |
|
|
Term
| Because polypeptide chains are encoded by separate genes, the one gene one protein hypothesis changed to |
|
Definition
| one gene one polypeptide chain |
|
|
Term
|
Definition
a recessive genetic disease in which the hemoglobin is mutated (to HbS) and changes the shape of the RBC. The mutated hemoglobin differs by a single amino acid in the peptide chain
Adult - two alpha and beta chains
Mutation happens in the beta chain
HbA2 has two alpha and two delta chains |
|
|
Term
|
Definition
| the order of nucleotides in a gene correlates directly with the order of amino acids in the corresponding polypeptide |
|
|
Term
|
Definition
| a carboxyl group group, amino group and an R group bounded to a simple carbon atom |
|
|
Term
|
Definition
| a dehydration reaction between the carboxyl group of one amino acid and the amino group of another. Releases water |
|
|
Term
| 4 levels of protein structure |
|
Definition
Primary - the sequence of amino acids
Secondary - folding configurations formed through interactions between neighboring amino acids(alpha helix, beta pleated sheet)
Tertiary - 3D conformation
Quaternary - position of multiple polypeptide chains in relation to each other |
|
|
Term
| posttranslationally modification definition |
|
Definition
| polypeptide chains that are modified after they've been synthesized |
|
|
Term
| possible posttranslationally modifications |
|
Definition
Removlal of N-terminus amino acid
Phosphorylation, acetylation or methylation of amino acids
Addition of carbohydrate chains
Removal of signal sequence
Cleavage of polypeptide chains |
|
|
Term
|
Definition
|
|
Term
|
Definition
| contractile proteins found in tissue |
|
|
Term
|
Definition
| portions of the protein that fold independently of the rest of the protein which have different functionalities |
|
|
Term
|
Definition
| the process where exons present in ancestral genes were brought together and recombined during evolution |
|
|
Term
|
Definition
| the portion of the genome that is involved in the production of rRNA |
|
|
Term
| Amino acids are divided into what groups |
|
Definition
| nonpolar, polar hydrophilic, polar positively charged and polar negatively charged |
|
|
Term
| Ribosomal size of prokaryotes and eukaryotes |
|
Definition
Pro - 70s
Eukaryotic - 80s |
|
|
Term
| rRNA component of prokaryotes |
|
Definition
23s rRNA
16s rRNA
5s rRNA
31 proteins |
|
|
Term
| rRNA component of eukaryotes |
|
Definition
28s srRNA
5s rRNA
5.8 rRNA
18s rRNA
46 proteins |
|
|
Term
|
Definition
Amino is converted to a different acid after being converted by ATP
A covalent bond forms between the 5' phosphate group of ATP and the carboxyl end of the amino acid with the help of synthetase
Amino acids bonds to the 3' end of the tRNA |
|
|
Term
|
Definition
| a short chain of about 30 amino acids present at the N-terminal end of some proteins; it functions to direct the protein to its final destination in the cell. |
|
|
Term
|
Definition
| refers to the joining of DNA molecules usually from different sources that aren't found together in nature |
|
|
Term
| Recombinant DNA procedure |
|
Definition
generating specific DNA fragments using restriction enzymes
joining these fragments with a vector
transferring the recombinant DNA molecule to a host cell to produce many copies that can be recovered from the host cell |
|
|
Term
|
Definition
| recovered copies of a recombinant DNA molecule |
|
|
Term
|
Definition
| Cut DNA at Specific Recognition Sequences |
|
|
Term
| Palindromic recognition sequences |
|
Definition
| nucleotide sequence reads the same on both strands of DNA in the 5' to 3' direction |
|
|
Term
|
Definition
| joines restriction fragments together to produce intact DNA molecules |
|
|
Term
|
Definition
| are carrier DNA molecules that can replicate cloned DNA fragments in a host cell. Needs several restriction enzyme sites to allow insertion of a DNA fragment |
|
|
Term
|
Definition
an extrachromosomal double-stranded DNA molecule that replicates autonomously in bacterial cells. A tyoe of vector
Has restriction enzyme sites
Has a marker gene that marks the host cell |
|
|
Term
|
Definition
Central third of lambda phage vectors can be replaced with foreign DNA and it can still infect and replicate inside cells.
Can hold up to 20 kb of cloned DNA |
|
|
Term
|
Definition
A vector that is created by combining parts of a lambda phage and parts of plasmids
Can replicate inside bacteria and can hold almost 50 kb of inserted DNA |
|
|
Term
| Bacterial artificial chromosomes (BACs) are based on |
|
Definition
| F factor and can carry up to 300 kb of inserted DNA . |
|
|
Term
| Yeast artificial chromosomes (YACs) can contain |
|
Definition
| 100–1000 kb of inserted DNA. |
|
|
Term
|
Definition
| are engineered to express a gene of interest to produce large quantities of the encoded protein. |
|
|
Term
| Yeast is widely used as a host for DNA cloning because: |
|
Definition
it can be grown easily
its genetics have been studied intensively
its genome has been sequenced
it can post-translationally modify eukaryotic proteins
it is considered to be safe |
|
|
Term
| DNA can be transferred to mammalian cells by |
|
Definition
| endocytosis and encapsulation in liposomes |
|
|
Term
| Polymerase Chain Reaction (PCR): |
|
Definition
| copies a specific DNA sequence through in vitro reactions that can amplify target DNA sequences present in very small quantities. |
|
|
Term
|
Definition
Denature
primer annealing
extension
two oligonucleotide primers that attaches to the 3' ends of both strands
The primers attach to denatured DNA and DNA polymerase copies the DNA
repeat whole process |
|
|
Term
|
Definition
| contains at least one copy of all the sequences in the genome of interest. Created by cutting genomic DNA with a restriction enzyme and ligating the fragments into vectos |
|
|
Term
| Chromosome-specific libraries are |
|
Definition
| libraries made from subgenomic amount of DNA such as a single chromosome |
|
|
Term
|
Definition
| contains complementary DNA copies made from the mRNAs present in a cell population and represents the genes that are transcriptionally active at the time the cells were collected for mRNA isolation |
|
|
Term
| A cDNA library is prepared by: |
|
Definition
isolating mRNA from cells
synthesizing the complementary DNA using reverse transcriptase
cloning the cDNA molecules into a vector |
|
|
Term
| Reverse transcriptase PCR can be used to generate cDNA from mRNA by |
|
Definition
first making a single-stranded cDNA copy of the mRNAs using reverse transcriptase
then using PCR to copy the single-stranded DNA into double-stranded DNA |
|
|
Term
|
Definition
| any DNA or RNA sequence that is complementary to some part of a cloned sequence present in the library (the target gene to be identified) |
|
|
Term
| Screening a plasmid library process |
|
Definition
Colonies are put on top of a filter
Colonies are lysed and the DNA is denatured
A DNA probe is added to the colonies and if any of the DNA on the film is complementary to the probe, a hybrid DNA-DNA molecule will form.
The film is removed and washed
The hybrids are detected by using X ray film which marks where hybridization takes place
The X ray film will then be used to determine which cells from the colonies hybridized |
|
|
Term
|
Definition
| establishes the number and order of restriction sites and the distance between restriction sites on a cloned DNA segment |
|
|
Term
|
Definition
| is used to identify which clones in a library contain a given DNA sequence and to characterize the size of the fragments from restriction digest. |
|
|
Term
|
Definition
cut DNA into segments and load into agarose gel for electrophoresis
Denature DNA and using paper towels, buffer, and a sponge, transfer the DNA onto filter.
Hybridize DNA on filter with radioactive probe
Wash excess probe out
The hybridized fragments show up as bands when paired with an X ray film |
|
|
Term
| The most common of DNA sequencing is |
|
Definition
|
|
Term
| Sanger sequencing technique |
|
Definition
Takes advantage of the fact that dideoxynucleotides have an H instead of an OH at the 3' position which terminates DNA synthesis because polymerase can only add to an 'OH group
A primer is bound to a template strand
DNA pol, dNTPS and ddNTPS are added
While the reaction is happening, DNA pol will accidentally add a ddNTP instead of a dNTPS which terminates synthesis.
As a result, strands that formed will have different lengths
The strands from the end of the primer on are then analyzed |
|
|
Term
| zwhat makes a restriction enzyme end sticky? |
|
Definition
| single-stranded complementary tails |
|
|
Term
|
Definition
| a region that has a large number of restriction enzymes |
|
|
Term
|
Definition
| RNA blotting. RNA is separated in the gel and probed with the labeled DNA |
|
|
Term
|
Definition
| plasmid, cosmid, lambda phage |
|
|
Term
| An ideal vector should have |
|
Definition
1) The capability to replicate inside the host cell
2) Should contain several restriction enzyme sites
3) Should be able to carry a large piece of DNA
4) Should carry a marker gene to identify the cells that have taken up the vector, usually an antibiotic resistant gene is used as a marker. |
|
|
Term
| What advantage does pUC18 have in terms of recombinant DNA technology? |
|
Definition
| Small size, high copy number, polylinker in lacZ gene |
|
|
Term
|
Definition
| in bacteria, mRNA that can encode for multiple polypeptide chains |
|
|
Term
|
Definition
| in eukaryotes, mRNA that can only encode for one polypeptide chaine |
|
|
Term
|
Definition
| TATA binding protein, initiates transcription |
|
|
Term
|
Definition
-9: TATA box
-35: TTGACA
-20: between consensus region of a promoter |
|
|
Term
|
Definition
| involved in transcription termination |
|
|
Term
|
Definition
| one of the most recognizable satellite DNA sequences found in the centromere regions |
|
|
