Genetics Exam Iii

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the study of genomes in their entirety

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genomics

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cloning the entire genome of a selected organism

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genome project

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considers the genomes of closely and distantly related species for evolutionary insight and enables conserved sequences to be used as a guide to analyzing gene function

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comparative genomics

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uses an expanding variety of methods, including reverse genetics, to understand gene function and to delineate networks of interacting genes and proteins in biological processes

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functional genomics

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analyzes the information content of entire genomes. this information includes numbers and types of genes and gene products, as well as binding sites on DNA and RNA that allow functional products to be produced at the correct time and place

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bioinformatics

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building up all of the individual reads into a consensus sequence

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sequence assembly

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a sequence for which there is consensus (or agreement) that it is an authentic representation of the sequence for each of the DNA molecules in that genome

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consensus sequence

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collections of short segments of DNA, representing the entire genome

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genomic libraries

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accessory chromosomes (non-essential elements such as plasmids, modified bacterial viruses, or artificial chromosomes) and propagated in microbes, usually bacteria or yeast--carry DNA inserts

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vectors

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sequences that are touching

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sequence contigs

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sequence reads from opposite ends of the genomic inserts in the same clone

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paired-end reads

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gapped collections of joined-together sequence contigs

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scaffolds (supercontigs)

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ordered and oriented set of clones covering the whole genome

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physical map

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the study of information content of genomes is called

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bioinformatics

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inventory of all the polypeptides encoded by an organism's genome

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proteome

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identification of all the functional elements of the genome

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annotation

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short strands of sequenced cDNA that can be used to determine the boundaries of the transcript

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expressed sequence tags (ESTs)

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ORFs or partial ORFs that may at first appear to be genes but are either nonfunctional or inactive due to the manner of their origin or to mutations

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pseudogenes

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DNA sequences that have been reverse-transcribed from RNA and randomly inserted into the genome

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processed pseudogenes

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most closely related genes

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homologs

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homologs that are the same locus inhereted from a common ancestor

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orthologs

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genes that belong to families that have expanded (and contracted) in number in the course of evolution. genes that are related by gene duplication events in a genome are called

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paralogs

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the order of genes within variously sized blocks is the same as their order in the most recent common ancestor of the two species

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synteny

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global approach to the study of the function, expression, and interaction of gene products

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functional genomics

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samples of DNA laid out as a series of microscopic spots bound to a glass "chip" the size of a microscope cover slide

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microarray

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detects physical interactions between two proteins

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two-hybrid test

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most widely used method of studying DNA-protein interactions

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ChIP (for chromatin immunoprecipitation)

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new discipline spawned from from genomics and the other "omics" where people try to put the parts together to understand the whole as a system

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systems biology

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phenominon that results in gene and trans-gene silencing and viral resistance through the production of siRNAs is called

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RNA interference

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targeting the protein for phenocopying on a genomic-scale

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chemical genetics

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a phenotype characterized by frequent reversion either somatically or germinally or both due to the interaction of transposable elements with a host gene

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unstable phenotype

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describes what a transposable element does when it leaves a chromosomal location. also celled transpose

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excise

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require no other elements for their mobility

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autonomous elements

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segments of of bacterial DNA that can move from one position on a chromosome to a different position on the same chromosome or on a different chromosome

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insertion-sequence (IS) elements

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an enzyme required for the movement of IS elements from one site in the chromosome to another

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transposase

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plasmids carrying genes that encode resistance to several antibiotics

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R factors

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mobile genetic element (where R factors reside)

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transposon (Tn)

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contain a variety of genes that reside b/t two nearly identical IS elements that are oriented in opposite direction

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composite transposons

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sequence formed by two nearly identical IS elements oriented in opposite direction in composite transposons

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inverted repeat (IR) sequence

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flanked by IR sequences, but these sequences are short (<50 bp) and do not encode the transposase enzyme that is necessary for transposition. thus, their mobility is not due to an association with IS elements.

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simple transposons

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virtually all transposable elements (prokaryotes & eukaryotes) are flanked by these

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target-site duplication

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most transposable elements in prokaryotes employ one of these two mechanisms

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replicative and conservative

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also called "cut-and-paste" in prokaryotes

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conservative pathway

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fused circle formed in replicative transposition

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cointegrate

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a single-stranded RNA virus that employs a double-stranded DNA intermediate for replication. eukaryotic retrotransposon elements look like this

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retrovirus

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RNA is copied into DNA by the enzyme

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reverse transcriptase

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when integrated into host chromosomes as double-stranded DNA, the double-stranded DNA copy of the retroviral genome is called a

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provirus

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both retroviruses and retrotransposons are flanked by _______ that are several hundred base pairs long

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long terminal repeats (LTRs)

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class 1 transposable elements

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retrotransposons

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retrotransposons such as Ty1 that have long terminal repeats at their ends are called

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LTR-retrotransposons

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class 2 elements

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DNA transposons

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a phenomenon that occurs when females from laboratory strains of D. melanogaster are mated with male derived from natural populations

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hybrid dysgenesis

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biologically deficient

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dysgenic

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when mutant gene is marked by the presence of the P element

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transposon tagging

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the vast majority of the transposable elements that make up the human genome are

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long interspersed elements, or LINEs and short interspersed elements, or SINEs

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can be best described as nonautonomous LINEs, because they have the structural features of LINEs but do not encode their own reverse transcriptase

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SINEs (short interspersed elements)

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the most abundant SINE in humans is called

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Alu

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the ability of some transposons to insert preferentially into certain sequences or genomic regions is called

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targeting

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certain agents that increase teh rate at which mutations occur

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mutagens

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several forms in which DNA bases can occur

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tautomers

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rare imino form of cytosine paires with

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adenine

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rare imino form of adenine pairs with

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cytosine

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rare enol form of thymine pairs with

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guanine

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rare enol form of guanine pairs with

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thymine

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naturally occuring damage to the DNA

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spontaneous lesions

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two autosomal recessive diseases in humans, xeroderma pigmentosum (XP) and Cockayne syndrome are caoused by defects in

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nucleotide-excision repair

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bypassing system in E.coli

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SOS system