genomics and epigenetics conceptual

exam 1

genome

the complete set of genes of an organism

transcriptome

set of expressed genes

epigenome

consists of chemical compounds that modify or mark the genome in a way that tells it what to do, where to do it, and when to do it

genetic mapping

the process of determining the location and chemical sequence of specific genes on specific chromosomes.

restriction map

type of genetic mapping that is constructed by cleaving DNA into fragments with restriction enzymes and measuring the distances between the sites. limited in terms of the length of DNA that can be represented

sequence map

type of genetic mapping that is the sequence of DNA from which the distance between genes can be accurately detected

polymorphism

refers to the simultaneous occurrence in the population of genomes showing variations at a given position (alleles producing different phenotypes)

1

polymorphism should be found at a frequency greater than __% in the population

phenotypic

polymorphism is detected at the \__________ level when a sequence affects gene function

restriction level fragmentation

polymorphism is detected at the \___________ level when a sequence affects a restriction enzyme target site

sequence

polymorphism is detected at the \___________ level through direct analysis of DNA

single nucleotide polymorphism (SNP)

a polymorphism caused by a change in a single nucleotide, responsible for most of the genetic variation between individuals

restriction fragment length polymorphism (RFLP)

inherited differences in cleave sites for restriction enzymes that result in differences in the lengths of the fragments produced by cleavage with relevant restriction enzymes. used for genetic mapping to link the genome direction to a conventional genetic marker.

haplotype

particular combination of alleles in a defined region of some chromosome.

non-repetitive sequence

characteristic of a genome where the haploid genome only contains one copy of the sequence

moderately-repetitive sequence

characteristic of a genome where multiple copies are found that may be identical or related. includes transposons

highly-repetitive sequence

characteristic of a genome where sequences are very short and present in a large number of copies; often tandem repeats

mitochondria, chloroplasts

these two organelles have genomes that show mendelian inheritance (maternally inherited)

low

in any given cell, most cells genes are expressed at a \_________ level

basal expression

expression level of a gene that is considered normal

gene family

set of genes whose exons are related

gene cluster

a group of adjacent genes that are identical or related

dna fingerprinting

analysis of sections of DNA that have little or no known function, but vary widely from one individual to another, in order to identify individuals

intron

intervening sequences that are spliced out of the primary transcript; usually non-coding

exon

found in mature RNA; coding portions of the DNA

intergenic dna

Non-coding DNA found between genes

intragenic dna

Non-coding DNA found within genes

non-coding dna

DNA that does not code for a protein

chromosome

a discrete unit of the genome carrying many genes

gene

the segment of DNA specifying production of a polypeptide chain; it includes regions preceding and following the coding regions as well as introns between the exons (coding regions)

allele

one of several alternative forms of a gene occupying a given locus on a chromosome

locus

the position on a chromosome at which the gene for a particular trait resides

linkage

the tendency of genes to be inherited together as a result of their location on the same chromosome

Loss of function mutation

mutation that results in the lost or reduced activity of a gene

gain of function mutation

mutation that results in an increase to the normal gene activity

proteome

complete set of proteins expressed

cis-acting sites

sites are configured such that two sites are on the same DNA molecule; the site affects the activity only of sequences on its own molecule of DNA (or RNA) - usually does not code for protein

trans-acting sites

two sites are configured such that they are present on different molecules of DNA (chromosomes)

superfamily

set of genes all related by presumed descent from a common ancestor, but now showing considerable variation

genome mapping

a map that can include a variety of types of maps that describe the set up and resulting organization of the genome

phenotype

the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.

genotype

an organism's genetic makeup, or allele combinations.

indel

Mutations defined by either the Insertion or Deletion of nucleotides in the genome; can range in size from 1 nucleotide to millions of nucleotides. Includes copy number variants and gene deletions.

whole genome duplication

Rare mutational event in which the chromosome number is doubled or fails to be reduced during cell division. Much more common are subgenomic duplication events where smaller chromosomal regions are duplicated. Often these smaller regions contain one or more genes.

pseudogenes

Nonfunctional genes in the genome that are no longer expressed in any member of the species.

sub-genomic duplication

duplication of part of the genome but not of the entire genome, more common than whole genome duplication

redundancy

the concept that two or more genes may fulfill the same function so that no single one of them is essential

copy number variants

variations found in the populations' genome that represent multiple copies of the same gene

histone acetyl transferases

enzymes that add acetyl groups to histone tail lysines, thereby opening chromatin

histone deacetylases

proteins that function to remove the acetyl groups from histones

make the chromatin in a more closed conformation

overal decreases the gene expression levels of the cell

silenced

a gene whose expression is turned off, commonly by negative transcription factors or epigenetic modifications such as methylation or histone deacetylation

dna methyltransferase

enzyme that transfers a methyl group from donor molecule to DNA

cpg islands

regions within the genome that are rich is C and G nucleotides which are sensitive to methylation

hypomethylation

Reduced methylation of DNA. This results in the activation of oncogenes genes and the resulting formation of tumours.

hypermethylation

an increase in the epigenetic methylation of cytosine and adenosine residues in DNA.

dna microarray chips

prepared experimental chips that contain complementary RNA to the mRNA of a variety of genes for which scientist wishes to screen expression levels

open reading frame

AUG followed by a number of codons and a stop codon in the same reading frame; region on a plasmid or vector where duplication of the DNA initiates

promoter region

before the gene of interest; represents the location where RNA polymerase and associated proteins will bind and initiate transcription

nonsense mutation

type of mutation where a normal codon is changed into a stop codon

missense mutation

type of mutation that results in different amino acids being encoded at a particular position in the resulting protein

silent mutation

type of mutation where the change of a single DNA nucleotide within a protein-coding portion of a gene does not affect the sequence of amino acids that make up the gene's protein.

heterochromatin

chromatin that is dense, transcriptionally inactive

euchromatin

chromatin that is loose, transcriptionally active

epigenetics

study of heritable and stable changes in gene expression that occur through alterations in the chromosome rather than in the DNA sequence