UAB Exam 3 Genetics

induced pluripotent stem cells (iPSCs)

Adult cells that have been artificially induced to dedifferentiate and revert to pluripotent stem cells capable of becoming many types of cells.

epigenome

All epigenetic modifications within the genome of an individual organism.

epialleles

Alleles that do not differ in their base sequence but have epigenetic differences that produce heritable variations in phenotypes.

metagenomics

An emerging field of genetics in which the genome sequences of a group of organisms inhabiting a common environment are sampled and determined.

zinc-finger nucleases

An engineered nuclease consisting of an array of zinc-finger domains attached to a restriction enzyme.

transcription activator-like effector nuclease (TALEN)

An engineered nuclease in which a protein of a type that normally binds to promoters is attached to a restriction enzyme.

functional genomics

Area of genomics that studies the functions of the genetic information contained within genomes.

structural genomics

Area of genomics that studies the organization and sequence of information contained within genomes; sometimes used by protein chemists to refer to the determination of the three-dimensional structure of proteins.

DNase I hypersensitive sites

Chromatin region that becomes sensitive to digestion by the enzyme DNase I.

yeast artificial chromosome (YAC)

Cloning vector consisting of a DNA molecule with a yeast origin of replication, a pair of telomeres, and a centromere. YACs can carry very large pieces of DNA (as large as several hundred thousand base pairs) and replicate and segregate as yeast chromosomes do.

cosmids

Cloning vector consisting of a plasmid packaged in a viral protein coat that can be transferred to bacteria by viral infection; can carry large pieces of DNA into bacteria.

expression vector

Cloning vector containing DNA sequences such as a promoter, a ribosome-binding site, and transcription initiation and termination sites that allow DNA fragments inserted into the vector to be transcribed and translated.

bacterial artificial chromosome

Cloning vector used in bacteria that is capable of carrying DNA fragments as large as 500 kb.

genomic library

Collection of bacterial colonies or phages containing DNA fragments that constitute the entire genome of an organism.

DNA library

Collection of clones containing all the DNA fragments from one source.

cDNA library

Collection of clones containing all the DNA fragments from one source.

comparative genomics

Comparative studies of the genomes of different organisms.

microbiome

Complete set of all bacteria found in a particular environment; for example, the human microbiome consists of all bacteria found in and on the human body.

interactome

Complete set of protein interactions in a cell.

mediator

Complex of proteins that is one of the components of the basal transcription apparatus.

CpG islands

DNA region that contains many copies of a cytosine base followed by a guanine base; often found near transcription start sites in eukaryotic DNA. The cytosine bases in CpG islands are commonly methylated when genes are inactive but are demethylated before the initiation of transcription.

response elements

DNA sequence shared by the promoters or enhancers of several eukaryotic genes to which a regulatory protein can bind to stimulate the coordinate transcription of those genes

insulators

DNA sequence that blocks, or insulates, the effect of an enhancer; must be located between the enhancer and the promoter to have blocking activity; may also limit the spread of changes in chromatin structure

SR protein

Group of serine- and arginine-rich proteins that regulate alternative splicing of pre-mRNA.

epigenetic marks

Heritable change in DNA or chromatin structure that does not involve alteration of the base sequence and that brings about changes in gene expression.

orthologs

Homologous genes found in different species that evolved from the same gene in a common ancestor.

paralogs

Homologous genes in the same species that arose through the duplication of a single ancestral gene.

transcription

Much of gene regulation in bacterial cells is at the level of _________________.

pluripotent

The property of being undifferentiated, with the capacity to form every type of cell in an organism.

forward genetics

Traditional approach to the study of gene function that begins with a mutant phenotype and proceeds to a gene that encodes the phenotype.

stem cells

Undifferentiated cell that is capable of forming every type of cell in an organism.

affinity capture

Use of an antibody to capture one protein from a complex mixture of proteins. The captured protein will "pull down" with it any proteins with which it interacts, which can then be analyzed by mass spectrometry to identify the proteins.

gene therapy

Use of recombinant DNA to treat a disease or disorder by altering the genetic makeup of the patient's cells.

microsatellites (short tandem repeats)

Very short DNA sequence repeated in tandem; also called a short tandem repeat

genetic engineering

a set of technologies that humans use to alter the genetic instructions of an organism by substituting DNA molecules

Taq polymerase

polymerase DNA polymerase commonly used in PCR reactions. Isolated from the bacterium Thermus aquaticus, the enzyme is stable at high temperatures, so it is not denatured during the strand-separation step of the cycle.

heat-shock proteins

proteins produced by many cells in response to extreme heat and other stresses that helps the cells prevent damage from such stressing agents

Recombinant DNA technology

set of molecular techniques for locating, isolating, altering, and studying DNA segments

activators

stimulate transcription through positive control

transcriptional regulator proteins

bind to enhancers, causing the formation of a loop in the DNA, which brings the promoter and enhancer into close proximity

single nucleotide polymorphism (SNP)

A single-base-pair difference in DNA sequence between individual members of a species.

haplotype

A specific set of linked genetic variants or alleles on a single chromosome or on part of a chromosome.

genome-wide association studies

A study that looks for nonrandom associations between the presence of a trait and alleles at many different loci scattered across a genome—that is, for associations between traits and particular suites of alleles in a population.

polymerase chain reaction (PCR)

A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides.

Levels of gene regulation in eukaryotes

chromatin structure, transcription, mRNA processing, translation, RNA stability, and posttranslational modification of proteins

chromatin remodeling complexes

complex of proteins that alters chromatin structure without acetylating histone proteins

condensed chromatin

contains tightly coiled strands of DNA that repress gene expression

transgene

Foreign gene or other DNA fragment carried in germline DNA.

gene deserts

A region of a genome that is gene poor—that is, a long stretch of DNA, possibly consisting of hundreds of thousands to millions of base pairs, that is completely devoid of any known genes or other functional sequences.

synthetics biology

A field that seeks to design organisms that might provide functions useful to humanity.

RNA sequencing

A method in which cDNA molecules are copied from the RNA molecules present in a cell and sequenced.

reverse genetics

A molecular approach to the study of gene function that begins with a genotype (a DNA sequence) and proceeds to the phenotype by altering the sequence or by inhibiting its expression.

CRISPR-Cas system

A molecular tool used for precise editing of DNA that relies on the action of CRISPR RNAs and Cas proteins

copy number variation (CNV)

Difference among individual organisms in the number of copies of any large DNA sequence (larger than 1000 bp).

segmental duplications

Duplicated chromosome segments larger than 1000 bp.

restriction enzymes

Enzyme that recognizes particular base sequences in DNA and makes double-stranded cuts nearby; also called a restriction endonuclease.

paramutation

Epigenetic change in which one allele of a genotype alters the expression of another allele; the altered expression persists for several generations, even after the altering allele is no longer present.

homologous genes

Evolutionarily related genes descended from a gene in a common ancestor.

targeted mutagenesis

Induction of mutations in particular DNA sequences to study their effects.

gene cloning

Insertion of DNA fragments into bacteria in such a way that the fragments will be stable and will be copied by the bacteria.

bioinformatics

Interdisciplinary field that combines molecular biology and computer science; develops databases and computational tools to store, retrieve, and analyze nucleic acid-and protein-sequence data.

probe

Known sequence of DNA or RNA that is complementary to a sequence of interest and will pair with it; used to find specific DNA sequences.

protein microarrays

Large number of different proteins applied to a solid support as a series of spots, each containing a different protein; used to analyze protein-protein interactions.

Ti plasmid

Large plasmid isolated from the bacterium Agrobacterium tumefaciens and used to transfer genes to plant cells.

annotated

Linking of the sequence information of a gene that has been identified to other information about the gene's function and expression, about the protein encoded by the gene, and about similar genes in other species.

physical maps

Map of physical distances between loci, genetic markers, or other chromosome segments; measured in base pairs.

genetic maps

Map of the relative distances between genetic loci, markers, or other chromosome regions determined by rates of recombination; measured in recombination frequencies or map units.

mutagenesis screen

Method for identifying genes that influence a specific phenotype. Random mutations are induced in a population of organisms, and individual organisms with mutant phenotypes are identified. These individual organisms are crossed to determine the genetic basis of the phenotype and to map the location of mutations that cause the phenotype.

mass spectrometry

Method for precisely determining the mass of a molecule by using the migration rate of an ionized molecule in an electrical field.

two-dimensional polyacrylamide gel electrophoresis (2D-PAGE)

Method for separating proteins in which the proteins are separated in one dimension by charge, separated in a second dimension by mass, and then stained. Each of the resulting spots is proportional to the amount of protein present.

chromosome walking

Method of locating a gene by using partly overlapping genomic clones to move in steps from a previously cloned, linked gene to the gene of interest.

whole-genome shotgun sequencing

Method of sequencing a genome in which sequenced fragments are assembled into the correct sequence in contigs by using only the overlaps in sequence.

map-based sequencing

Method of sequencing a genome in which sequenced fragments are assembled into the correct sequence in contigs with the use of genetic or physical maps.

oligonucleotide-directed mutagenesis

Method of site-directed mutagenesis that uses an oligonucleotide to introduce a mutant sequence into a DNA molecule.

positional cloning

Method that allows for the isolation and identification of a gene by examining the cosegregation of a phenotype with previously mapped genetic markers.

in situ hybridization

Method used to determine the chromosomal location of a gene or other specific DNA fragment or the tissue distribution of an mRNA by using a labeled probe that is complementary to the sequence of interest.

histone code

Modification of histone proteins, such as the addition or removal of phosphate groups, methyl groups, or acetyl groups, that encode information affecting how genes are expressed

real time PCR

Modification of the polymerase chain reaction that quantitatively determines the amount of starting nucleic acid; the amount of DNA amplified is measured as the reaction proceeds.

knockout mice

Mouse in which a normal gene has been disabled ("knocked out").

knock-in mice

Mouse that carries a foreign DNA sequence inserted at a specific chromosome location.

microarrays

Ordered array of DNA fragments, fixed to a solid support, which serve as probes to detect the presence of complementary sequences; often used to assess the expression of genes in various tissues and under different conditions.

Southern blotting

Process by which DNA is transferred from a gel to a solid support such as a nitrocellulose or nylon filter.

Northern blotting

Process by which RNA is transferred from a gel to a solid support such as a nitrocellulose or nylon filter.

Western blotting

Process by which protein is transferred from a gel to a solid support such as a nitrocellulose or nylon filter.

DNA sequencing

Process of determining the sequence of bases along a DNA molecule.

Human Proteome Project

Project with the goal of identifying and characterizing all proteins in the human body

engineered nucleases

Protein consisting of part of a restriction enzyme, which cleaves DNA, combined with another protein that recognizes and binds to a specific DNA sequence; capable of making double-stranded cuts to the DNA at a predetermined DNA sequence. Engineered nucleases can be custom designed to bind to and cut any particular DNA sequence.

inactivation center

Segment of the X chromosome at which inactivation of one X chromosome is initiated in female cells.

next generation sequencing technologies

Sequencing methods, such as pyrosequencing, that are capable of simultaneously determining the sequences of many DNA fragments; these technologies are much faster and less expensive than the Sanger dideoxy sequencing method.

transcriptome

Set of all RNA molecules transcribed from a genome.

proteome

Set of all proteins found in a cell.

multigene

Set of genes similar in sequence that arose through repeated duplication events and often encode different protein products.

contig

Set of overlapping DNA fragments that have been assembled in the correct order to form a continuous stretch of DNA sequence.

sticky ends

Short, single-stranded overhanging end on a DNA molecule produced when the DNA is cut by certain restriction enzymes; also called a sticky end. Cohesive ends are complementary and can spontaneously pair to rejoin DNA fragments that have been cut with the same restriction enzyme.

tag-SNPs

Single-nucleotide polymorphism used to identify a haplotype.

linkers

Small synthetic DNA fragment that contains one or more restriction sites; can be attached to the ends of any piece of DNA and used to insert it into a plasmid vector.

ddNTPS

Special substrate for DNA synthesis used in the Sanger dideoxy sequencing method; identical with dNTP (the usual substrate for DNA synthesis) except that it lacks a 3′-OH group. The incorporation of a ddNTP into DNA terminates DNA synthesis.

cloning vector

Stable, replicating DNA molecule to which a foreign DNA fragment can be attached for transfer to a host cell.

genomics

Study of the content, organization, and function of genetic information in whole genomes.

transcriptomics

Study of the expression of the genome.

genetic conflict hypothesis

Suggestion that genomic imprinting evolved because different and conflicting pressures act on maternal and paternal alleles of genes that affect fetal growth. For example, paternally derived alleles often favor maximum fetal growth, whereas maternally derived alleles favor less than maximum fetal growth because of the high cost of fetal growth to the mother.

site-directed mutagenesis

Targeted mutagenesis technique used in bacteria in which a short sequence of nucleotides is cut out with restriction enzymes and replaced with a synthetic oligonucleotide.

gel electrophoresis

Technique for separating charged molecules (such as proteins or nucleic acids) on the basis of molecular size or charge, or both.

reverse transcription PCR

Technique that amplifies sequences corresponding to RNA; reverse transcriptase is used to convert RNA into complementary DNA, which can then be amplified by the usual polymerase chain reaction.

DNA fingerprinting

Technique used to identify individuals by examining their DNA sequences.

repressors

inhibit transcription through negative control

promoters

many eukaryotic genes have their own _________ and are transcribed independently of other genes

biotechnology

the use of biological processes, organisms, or systems to manufacture products intended to improve the quality of human life