Principles of Life, Chapter 12 Reading

________ requires a primer to begin polymerization.

DNA polymerase

________ are used for sequencing.

Templates

________ of the newly added nucleotide at each location is detected with a camera (color indicates which nucleotide was added)

Fluorescence

________ stranded DNA primers complementary to the adapter sequenced are used in PCR.

Single

________ are small, compact, usually have no introns, and carry plasmids along with their main chromosome.

Bacterial genomes

________ are denatured by heat and short, synthetic adapter sequences (oligonucleotides) are then attached to each end of each ________.

Fragments

________ sequencing allows DNA sequences of 300 to 1k bases to be obtained in a single reaction.

Sanger

A 3 ________ on the end nucleotide must be available on the growing strand for the addition of the next nucleotide.

OH group

________ varies in length, in one- nucleotide increments, labeled so the end nucleotide can be idd.

Product DNA

________ are heated to denature them; universal primer, polymerase, and four dNTPs are added (NOT ddNTPs)

DNA fragments

________ are much larger, have more regulatory sequences, and most DNA does not encode functional proteins, and the core /pan genomes are usually the same.

Eukaryotic genomes

Approximately ________ is made up of transposons and other repetitive sequences.

half of the genome

________ yield several kinds of information.

Genome sequences

Single- celled ________ and is the least complex of the eukaryotic model organisms.

eukaryotic microbe

The sequencing reaction is set up so that only one nucleotide at a time is addd to the ________ strand.

new DNA

________ are attachd to the surface of a solid support, leaving a small amount of space between each bolecule.

Fragments

An approach that begins with an interesting phenotype, finds the gene(s) underlying it, and then determines as much as possible about those genes

Forward Genetics

An approach that begins with a gene and attempts to determine its function, often by examining what happens when the gene is knocked out

Reverse Genetics

Rapid DNA sequencing on a micro scale in which many fragments of DNA are sequenced in parallel

High-throughput sequencing

The subset of the genome that is expressed as RNA in a particular cell or tissue at a particular time

Transcriptome

The sequencing of all of the complementary DNA in a sample, obtained from the RNA by reverse transcription

RNA Sequencing

Sequences of DNA within genes that begin with a start codon and end with a stop codon

Open reading frames

The study of the proteome-the complete complement of proteins produced by an organism

Promteomics

The study of the metabolome (complete set of small molecules present) as it relates to the physiological state of a cell, tissue, or organism

Metabolomics

normal cellular process molecules

Primary

unique to specific groups of organisms

Secondary

The part of a genome found in all individuals (or strains) within a species

Core genome

The entirety of genome sequence found across all individuals (or strains) within a species

Pan genome

The practice of analyzing DNA from environmental samples without isolating intact organisms

Metagenomics

Mobile DNA segments that can insert into a chromosome and cause genetic change; do not use RNA intermediates; pretty much junk DNA

Transposons

Homologous genes whose divergence can be traced to speciation events

Orthologs

A DNA segment that is homologous to a functional gene but is not expressed because of changes to its sequence or changes to its location in the genome

Pseudogene

Homologous genes whose divergence can be traced to gene duplication events

Paralogs

A set of similar genes derived from a single parent gene; need not be on the same chromosomes

Gene family

Simple 1-5 base pair DNA repeats, present in multiple tandem copies; also known as STRs or SSRs

Miscrosatellites

Mobile genetic elements that are reverse transcribed into RNA as part of their transfer mechanism

Retrotransposons

Inherited variations in a single nucleotide base in DNA that differ between individuals

Single nucleotide polymorphisms (SNPs)

A small glass or plastic square onto which thousands of single-stranded DNA sequences are fixed so that hybridization of cell-derived RNA or DNA to the target sequences can be performed

DNA Microarray

A technique in which a single-stranded nucleic acid probe is made that is complementary to, and binds to, a target sequence, either DNA or RNA

Nucleic Acid Hybridization

The use of an individuals genome sequence to inform ancestry determination, risks of genetic disease and response to drugs

Personal genomics

The study of how an individual's genetic makeup affects their response to drugs or other agents, with the goal of predicting the effectiveness of different treatment options

Pharmacogenomics