Combo with "Genetics Ch 5 Genetic Linkage and Mapping in Eukaryotes" and 14 others

parental ditypes (PD)

-Assuming no crossover between the homologs, ascospores produced by one of these arrangements contain the same alleles as the original parent strains -also 2-strand double crossover [no recombination]

second-division segregation pattern

-In a heterozygous meiocyte, if a crossover occurs between the gene and the centromere, the alleles segregate at meiosis II when sister chromatids segregate each ascus contains 4 parentals and 4 recombinant spores

In lab studies, the ascospores can be removed from the ascus and cultured to determine their genotypes; this process is called-

tetrad analysis

If a single crossover occurs between either of the homolog pairs, a _______ is produced, containing two parental spores and two nonparental spores

tetratype (TT)

Yeast artificial chromosome

The first artificial chromosomes developed:

odds ratio

-numerator=likelihood that distribution of genotypes and phenotypes in pedigree is produced by genetic linkage -denominator=chance that it is produced by independent assortment

Creighton and McClintock

-obtained cytological evidence that recombination between the genes was accompanied by physical exchange between the homologs -fragment on one end of chromosome knob on other

What is a genetic screen?

A procedure where a population is mutagenized and the progeny are examined for mutant phenotypes

Multiple cloning sites

A vector DNA sequence containing several unique restriction enzyme target sequences facilitating cloning of inserted DNA fragments

produce a complimentary strand to the target molecule and detect which bases are addded at each step. Millions of sequencing reactions can be run simultaneously, (high throughput) the DNA to be sequenced does not need to be known prior to sequencing. can sequence samples found in trace amounts, can sequence DNA that is difficult to clone

Advantages of next generation/third generation sequencing (4):

DNA doesn't need to undergo cloning or PCR, it is faster, it is cheaper

Advantages of third generation sequencing over next generation sequencing (3):

Primer walking or shotgun sequencing

After cloning a DNA fragment, one of these two methods can be used to sequence the DNA fragment to know what the nucleotide bases are:

Yes

Can blunt end DNA molecules be recombined?

100-200 kb

Capacity of a BAC

250-2000 kb

Capacity of a YAC

Under 15 kb

Capacity of a plasmid for insert sequences:

Under 23 kb

Capacity of linear phage chromosomes for insert sequences:

YAC's

Do BAC's or YAC's carry a larger insert size?

syntenic genes

Genes located on the same chromosome -so close together that alleles cannot assort independently

______ suggested that nonparental allele combinations resulted from recombination between the X chromosomes of the heterozygous female parent

Morgan -X linked gene for eye/wing in Drosophila

Using molecular probes

How are DNA libraries screened for specific DNA sequences?

interference [I]

I=1-c -the double crossovers expected but not produced -negative interference produces more double crossovers than expected

Double digest

In restriction mapping, in order to determine which order of restriction sites is correct, this must be performed:

Transformation

Recombinant DNA molecules are introduced into the bacteria by the process known as:

Sticky end

Short single-stranded overhangs created by the cleavage of DNA by specific restriction endonucleases, which can potentially base pair with complementary single stranded sequences

Shotgun sequencing

The sequencing method that relies on redundant sequencing of fragmented DNA in the hope that all regions will be sequenced at least a few times

Primer walking

The sequencing method that relies on the successive synthesis of primers based on the progressive attainment of new sequence information

Recombinant DNA technology

The set of techniques developed for amplifying, maintaining, and manipulating specific DNA sequences

Those derived from the genomic DNA of an organism (genomic lib), and those derived from mRNA

The two types of DNA libraries:

Genomic library

The type of DNA library consisting of genomic DNA

Complementary DNA library (cDNA library)

The type of DNA library consisting of mRNA

cDNA library

The type of DNA library that represents a subset of all the genes in the genome; represents only the expressed genes

Forward genetic analysis

The type of genetic analysis that starts with a genetic screen to identify specific phenotypic abnormalities in a population of organisms that have been mutagenized.

LacZ gene

What feature of the plasmid vector selects for only those bacteria that contain a recombinant plasmid and selects against nonrecombinant plasmids?

Add a Poly-dt primer for reverse transcriptase to use

What is the first step in making a cDNA library from mRNA?

Selects for only bacteria containing the plasmid

What is the purpose of a selectable marker in a plasmid vector?

Can only read about 1000 bp and most DNA regions of interest are much larger than this

Why can dideoxy sequencing not be used to sequence many DNA regions of interest?

transcription factors

a broad category of proteins that influence the ability of RNA polymerase to transcribe DNA into RNA.

true or false: The two parental types are approximately equal in frequency, as are the two recombinant types

TRUE

true or false: homologous crossover occurs sometimes during mitosis

TRUE

ordered ascus

arrangement of daughter spores reflects the orientation of alleles carried by each chromatid in metaphase I

linkage disequilibrium

certain haplotypes are maintained in a population, usually due to natural selection

_________ can be used to determine gene order

double recombinants, or double crossover -only one allele is different; this is the middle gene -list in each of 3 possible orders

Intragenic recombination

infrequent event in which crossing over occurs within a gene

tetratypes are [more/less] frequent than PD

less frequent -->NPD are even less frequent

The ascospores produced by the second arrangement will contain alleles in different combinations from the original parent strains, called a ______

nonparental ditype (NPD) -forming only when 4-strand double crossovers take place

coefficient of coincidence [c]=

observed double crossovers/expected double crossovers

GTF (general transcription factor)

one of several proteins that are necessary for basal transcription at the core promotor.

mapping function [based on Poisson distribution]

-does not account for interference -can be used to correlate the frequency of crossover with the actual number of crossover events

what crossover event is least frequent in 3-point test-cross?

-double crossover -both events must occur

an organism that exhibits complete linkage [rare]

-drosophila males have no crossing over

lod score

-logarithm of the odds ratio -determines theta value -sum all lod scores for each theta value to get Zmax -higher than 3.0=linkage at theta value -less than -2.0=significant evidence against genetic linkage -between -2.0 and 3.0 are inconclusive

when calculating recombination frequencies, for the larger distance, the double crossover progeny are-

-added twice because each represents 2 crossovers between them

three-point test-cross analysis

-allows you to map 3 linked genes simultaneously -

Genetic linkage

-can be quantified to map the positions of genes on chromosomes

Zmax

-corresponds to the recombination frequency that is most likely to be correct

theta value

-range 0-.50

upper limit to recombinant gametes-single crossovers

-single crossover produces 50% recombinant gametes and 50% parental -all 4 possible single crossovers result in same recombinant gametes

haplotype

-specific array of alleles in a set of linked genes on a single chromosome -these alleles tend to be passed on together during meiosis -may consist of any combination of linked genes with genetic variation

allelic phase

-the arrangement of alleles of linked genes on parental chromosomes -obstacle for mapping human genes -can be determined when disease-causing allele segregates with known genetic marker

why are genes that are closer together less likely to recombine?

-the closer the genes are, the less likely a recombination nodule will form between them

map units (m.u.) vs centiMorgan (cM) vs recombination frequency

1 m.u. = 1 cM = 1% recombination

Blunt ends

5' or 3' ends of double stranded DNA lacking any single stranded overhangs

what is recombination limit? why?

50% -Once genes are far enough apart to produce recombination frequencies of 50%, the pattern of segregation is that expected of independent assortment

Steps of a forward genetic screen

:Choose an organism, choose a mutagen, mutagenize the organism, screen for phenotypic defects, identify the gene sequence responsible for the mutation, analyse the molecular function of the gene

Vector

A carrier fragment of DNA with attributes that will allow amplification in a biological system

DNA library

A collection of cloned fragments of DNA (single source

DNA clone

A fragment of DNA that is inserted into a vector

Bacteria artificial chromosome

Cloning vector used in bacteria that utilizes the F plasmid origin of replication; can accept DNA inserts up to 500 kb

Yeast artificial chromosome

Cloning vector used in yeast that utilizes an endogenous yeast origin of replication, centromere and telomere; can accept DNA inserts in excess of 1 megabase

crossing over occurs at a ____ rate between genes that are further apart [lower/higher]

Crossing over occurs at a higher rate between genes that are farther apart, and a lower rate between genes that are closer together -higher rate = higher frequency

Mutagenesis

The process by which an organism is treated with a mutagen to create mutations throughout the genome

tetrad

The four ascospores in an ascus

Recombinant clone

The joining together of a cloning vector and donor DNA fragment produces a:

Molecular cloning

The method for DNA sequence amplification that does not require prior knowledge of the DNA sequence

PCR

The method that requires some prior knowledge of a DNA sequence that needs to be amplified

Within the lacZ gene

The multiple cloning site is often located here in a bacterial plasmid:

Bacteria artificial chromosome

The preferred artificial chromosome cloning vector

YAC

This cloning vector has the highest capacity

BAC

This cloning vector has the second highest capacity

Nonrecombinant DNA

This is created when the sticky ends of rejoin rather than incorporating a donor insert

Antibiotic resistance like ampicillan resistance

This is often the selectable marker in a plasmid vector:

Recombinant DNA technology

This provides the tools for proceeding from mutant phenotype to DNA sequence, so that alleleic differences can be examined at the molecular level

Restriction map

This shows the numbers and relative positions of target sites for restriction enzymes of a DNA molecule

Molecular cloning or PCR

To reproduce large amounts of individual pieces of DNA created by restriction enzymes, these two different processes can be used:

regulatory transcription factor

a protein or protein complex that binds to a regulatory element and influences the rate of transcription via RNA polymerase.

regulatory element (control element)

a sequence of DNA (or possibly RNA) that binds a regulatory protein and thereby influences gene expression. Bacterial operator sites and eukaryotic enhancers and silencers are examples.

what can affect recombination frequency?

age, environment, and sex -dietary levels of metal ions can affect crossover in flies

The diploid cells undergo meiosis to produce four haploid ______ in a sac called an _____

four haploid ASCOSPORES in a sac called an ASCUS

linkage equilibrium

genotype for a chromosome at one gene is expected to be independent of its genotype for other genes

Homologs that do not reshuffle alleles under study are called-

parental chromosomes or nonrecombinant chromosomes

Genetic linkage mapping-

plots the positions of genes on chromosomes

upper limit: Three-strand double crossovers

produce 50% parental and 50% recombinant gametes

upper limit: Two-strand double crossovers

produce ONLY PARENTAL gametes

upper limit: Four-strand double crossovers

produce all recombinant gametes -recombination LIMIT is 50%

crossing over occurs during-

prophase I of meiosis

r [recombination frequency]=

r= # recombinant gametes / total # meioses

recombination frequency=

r=[.5TT]+[NPD]/total tetrads -only half TT spores are recombinant

Alleles of syntenic genes can be reshuffled when crossing over occurs between homologs to produce ______________

recombinant chromosomes

gene regulation

the phenomenon in which the level of gene expression can vary under different conditions.