Genetics Exam 5

Human Genome Project

1990. 13 year effort.

ChIP-chip assay

A DNA microarray found on a chip

embryonic stem cells (ES cells)

Are in the early mammalian embryo, found in the inner cell mass of the blastocyst (preimplantation embryo).

biodegradation

Biotransformation resulting in a breakdown of the toxic pollutant into less complex, nontoxic metabolites.

multipotent

Can differentiate into many cell types, but not nearly as many as a ES cell. (Hematopoietic stem cells)

genome databases

Databases that focus on the genetic sequences and characteristics of a single species

tandem mass spec

Determines amino acid sequence of a given peptide using two mass specs

P1 artificial chromosomes (PACs)

Developed from P1 bacteriophage chromosomes

bacterial artificial chromosome (BACs)

Developed from bacterial F factors

GMOs

Genetically modified organisms. Organisms that have received genetic material via recombinant DNA technology.

in situ hybridization

Hybridization conducted on chromosomes that are being held in place.

sequencing by synthesis (SBS)

Involves the identification of each nucleotide immediately after it is incorporated into a DNA strand by DNA polymerase

locus (plural loci)

Refers to the site within a genetic map where a specific gene or other DNA segment is found

high-throughput sequencing

The ability to rapidly sequence large amounts of DNA

sequence-tagged site (STS)

The amplified region that occurs when a pair of PCR primers copies a single site within a set of chromosomes

T-DNA

The segment of DNA found within a Ti plasmid that is transferred from the bacterium to the infected plant cells. The T-DNA from the TI plasmid becomes integrated into the chromosomal DNA of the plant cell by recombination.

founder

The single organism that is the origin of a disease causing allele

gene replacement

The swapping of a cloned gene made experimentally with a normal chromosomal gene found in a living cell.

bioinformatics

The use of computers, mathematical tools, and statistical techniques to record, store, and analyze biological information.

genome

Total genetic composition of an organism or species

comparative genomics

Uses information from genome projects to understand the genetic variation among different populations.

linkage mapping

Uses the frequency of genetic recombination between different genes to determine their relative spacing and order along a chromosome.

pulsed-field gel electrophoresis (PFGE)

Using this method, large pieces of chromosomes or an entire small chromosome can be separated and identified using alternating pulses of electrical current at different angles

gene addition

When a cloned gene is introduced into a cell and becomes integrated into the genome by non-homologous recombination so that both the cloned and normal genes are present.

gene knockout

When a cloned gene is rendered inactive by mutation and replaces the normal gene, researchers can study how the loss of function gene function affects the organism. This is called a gene knockout.

gene redundancy

When one type of gene is inactivated, another gene with a similar function may be able to compensate for the inactive gene.

pattern recognition

a program that recognizes a pattern of symbols

DNA microarray/gene chip

a small silica, glass, or plastic slide that is dotted with many different sequences of DNA, each corresponding to a short sequence within a known gene.

codon bias

certain codons are used more frequently than others in an organism

Mass spec

determines identity of a protein by measuring mass of molecules, such as peptide fragments

restriction fragment length polymorphisms (RFLPs)

genetic variation within a population in the lengths of DNA fragments that are produced when chromosomes are digested with particular restriction enzymes

search-by-content

identifies sequences with a nucleotide content that differs significantly from a random distribution

ex vivo approach

in the case of gene therapy, refers to genetic manipulations that occur outside of the body the products are reintroduced into the body.

motif

name given to a domain or amino acid sequence that functions in a similar manner to many different proteins

monomorphic

term used to describe a gene that can be found as only one allele in a population

cluster analysis

the analysis of microarray data to determine if certain groups of genes are exposed under the same conditions

posttranslational covalent modification

the covalent attachment of a molecule to a protein after it has been synthesized via ribosomes

hybridization

the phenomenon in which two single stranded molecules renature together to form a hybrid molecule

subcloning

the procedure of making smaller DNA clones from a large one

homologous

two genes that are similar because they have been derived from the same ancestral gene

RNA editing

A change in the base sequence of an RNA after it has been transcribed

genetic map/chromosome map

A chart that describes the relative locations of genes or other DNA segments along a chromosome

chromosome walking

A common method used in positional cloning in which a mapped gene or RFLP marker provides a starting point to molecularly "walk" toward a gene of interest via overlapping clones.

gene knockin

A gene addition in which a gene of interest has been added to a particular site on the genome.

transgene

A gene that has been extracted from the DNA of one organism and transferred into the DNA of an organism of another species.

RFLP map

A linkage mao composed of many RFLP markers

molecular pharming

A recombinant technology that involves the production of medically important proteins in the mammary glands of livestock. Also, the manufacture of medical products by agricultural plants.

molecular marker

A segment of DNA found at specific site along a chromosome and has properties that enable it to be uniquely recognized using molecular tools such as polymerase chain reaction (PCR) and gel electrophoresis.

sequence element

A sequence with a specialized function

contig

A series of clones that contain contiguous, overlapping pieces of chromosomal DNA.

T-DNA Vectors

A small segment of T-DNA that is used as a carrier of another segment of DNA.

positional cloning

A strategy in which a gene is cloned based on its mapped position along a chromosome to find a segment of DNA with a certain gene.

totipotent

Can give rise to all cell types in an organism ( A fertilized egg).

pluripotent

Cells that can differentiate into almost every cell type of the body. However, a single ES cell has lost the ability to produce an entire, intact individual.

unipotent

Cells that can only differentiate into one cell type. (primordial germ cells)

artificial chromosomes

Cloning vectors that can accommodate much larger sizes of DNA inserts.

reproductive cloning

Methods that produce two or more genetically identical individuals.

functional genomics

Once a genome is known, researchers can examine at the level of many genes how the components of a genome interact to produce the traits of an organism.

Transgenic Organism

Organism that has received functional recombinant DNA from a different species.

embryonic carcinoma cells (EC cells)

Pluripotent cells that give rise to tetra-carcinomas. These bizarre tumors contain a variety of tissues including cartilage, neuroectoderm, muscle, bone, skin, ganglionic structures, and primitive glands.

antibody microarray

Purpose is to study expression

cytogenetic mapping

Relies on the localization of gene sequences within chromosomes that are viewed microscopically and are mapped cytogenetically according to banding pattern

genome-sequencing projects

Research endeavors that have the ultimate goal of determining the sequence of DNA bases of the entire genome of a gibe species

biotransformation

This occurs when enzymes produced by a microorganism modify a toxic pollutant by altering or transforming its structure.

isoelectric focusing

a protein migrates to the point in a gel during electrophoresis where its net charge is zero

open reading frame (ORF)

a region of nucleotide sequence that does not contain any stop codons

protein microarrays

proteins dotted on silica or glass slide

functional protein microarray

purified cellular proteins spotted on a microarray

sequence recognition

refers to a program that recognizes particular sequence elements

alternative splicing

refers to the phenomena in which a pre-mRNA can be spliced in more than one way

search-by-signal

relies on known sequences with a nucleotide content that differs significantly from a random distribution

two-dimensional gel electrophoresis

technique used to separate proteins

genomics

the molecular analysis of the entire genome of a species

orthologs

two homologous genes found in different species`

paralogs

two or more homologous genes found in a single species

cosmid

A hybrid between a plasmid vector and a phage. Its DNA can replicate in a cell like a plasmid or be packaged into a protein coat like a phage. Cosmid vectors can usually accept DNA fragments that are tens of thousands of base pairs in length

chromatin immunoprecipitation (ChIP)

A method for determining whether proteins bind to a particular region of DNA. This method analyzes DNA-protein interactions as they occur in the chromatin of living cells.

Chromosome painting

A method of differentiating between fluorescently labeled probes by assigning each of them a different color.

biolistic gene transfer

A method of producing transgenic plants in which plant cells are bombarded with high-velocity DNA coated microprojectiles that penetrate the cell wall and the membrane, thereby entering the plant cell.

physical mapping

An approach to mapping in which DNA-cloning techniques are used to determine the location of and distance between genes and other DNA regions. In a physical map, the distances are computed as the number of nucleotide base pairs between genes.

chimera

An organism that contains genetic information embryonically derived from two different organisms

polymorphic

As with alleles, molecular markers may vary between individuals within a population.

microsatellites/short tandem repeats (STRs)

Short, repetitive sequences that are abundantly interspersed throughout a species' genome and vary considerably in length among different individuals.

lod score method

Statistical test used by researchers to decide on the likelihood of linkage between to RFLPs (newton morton 1955)

stem cells

Supply the cells that construct our bodies from a fertilized egg.

next-generation sequencing technologies

Techniques that have superseded the Sanger dideoxy method method for large sequencing projects. (pyrosequencing)

Biotechnology

The application of technologies that involve the use of living organisms, or products from living organisms, for the development of products that benefit humans.

proteome

The entire collection of proteins a given cell or organism can make

mapping

The experimental process of determining locations of genes or other segments of DNA along individual chromosomes.

yeast artificial chromosome (YAC)

The first artificial chromosome

embryonic germ cells (EG cells)

The germ-line cells found in the gonads during the early fetal stage of development.

gene therapy

The introduction of cloned genes into living cells to treat disease.

proteomics

The long-term goal of researchers, study to determine the roles of all cellular proteins, as well as the interactions that these proteins experience, to produce the characteristics of particular cell types and the traits of complete organisms.

liposomes

The most common non viral technique of transferring a cloned gene into human cells is by the use of liposomes. It involves the use of DNA-liposomes(lipid vesicles) complexes that carry a positive charge and are taken into cells via endocytosis, in which a portion of the plasma membrane invaginated and creates an intracellular vesicle known as an endosome. The liposome is degraded in the endosome. The DNA is then released into the cytosol, imported into the nucleus, and then integrated into a chromosome of the target cell. Advantage: liposomes do not elicit an immune response. Disadvantage: efficiency of gene transfer may be low.

fluorescence in situ hybridization (FISH)

The most common technique of in situ hybridization involving the use of fluorescently labeled DNA probes.

shotgun sequencing

The most efficient and inexpensive way to sequence a genome in which DNA fragments to be sequenced are randomly generated from larger DNA fragments.

electroporation

The use of electrical current to create temporary pores in the plasma membrane

biological control

The use of living organisms or their products to alleviate plant diseases or damage from environmental conditions.

bioremediation

The use of living organisms or their products to decrease pollutants in the environment.

microinjection

The use of microscopic-sized needles to inject DNA into a cell