Difference between revisions of "Halorhabdus utahensis Genome"

Revision as of 02:19, 18 September 2008

This page will be used by Davidson College students in the Genomics Laboratory course.

RNA Genes

tRNA Genes Check List
rRNA operon
2 misc. RNA genes (short summary list)
References
Gene Annotation Template
General Questions
Page for Annotated Genes

Other Resources

Consensus Shine Dalgarno

This is a list of glossary words (A - Z):

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

B

C

carbon fixation - using carbon dioxide to create organic materials [1] (Samantha)

chemotaxis - the process in which cells move according to the presence of certain chemicals [2] (Nick)

COG (Cluster of Orthologous Groups)- corresponds to a highly conserved domain and generally consists of either individual proteins or groups of paralogs (COG Pallavi)

concatemer - long continuous DNA molecule that contains the same DNA sequence repeated in series [3](Samantha)

D

E

F

FASTA format - a text-based format for representing either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. The sequence name and other descriptors often precede the amino acide sequence. [4] (Nick)

G

glaucophyte - freshwater algae that have not been studied well [5](Samantha)

H

haemolysin or hemolysin - a chemical produced by a bacteria that can break down red blood cells [6] (Nick)

haplotype-collection of alleles that travel together (Lecture, Pallavi)

haptophyte - phylum of algae (Samantha)

heterokont - major line of eukaryotes consisting of about 10,500 known species, most of which are algae (Samantha)

homeobox - DNA sequence within transcription factor genes that allow the cell to respond to patterns of development by having the transcription factors switch on gene cascades (Samantha)

horizontal gene transfer-DNA transmission between species and incorporation of the DNA into the recipient's genome (horizontal gene transfer Pallavi)

hydrolase - an enzyme that catalyzes hydrolysis, the breakdown of water into oxygen and hydrogen atoms which often then continue to participate in other reactions [7] (Nick)

I

indole-a chemical compound that is produced from the break down of tryptophan (indole Pallavi)

inclusion body - Inclusion bodies are collections of stainable substances, usually proteins, that are found either in the nucleus or the cytoplasm. It is thought that these bodies are often the result of viral proteins that misfolded [8] (Nick)

isoelectric point - the pH at which a particular molecule or surface carries no net electrical charge [9] (Nick)

J

K

L

M

mycoplasma - genus of bacteria that lack a cell wall, making them resistant to many antibiotics that target cell wall synthesis [10] (Nick)

N

nucleomorph - reduced eukaryotic nuclei found in plastids (Samantha)

O

open reading frame (ORF)-a segment of DNA that can potentially encode for a protein and it begins with a start codon (usually ATG) ORF (Pallavi)

operon - a functioning unit of key nucleotide sequences including an operator, a common promoter, and one or more structural genes, which is controlled as a unit to produce messenger RNA (mRNA), in the process of protein transcription [11] (Nick)

optical mapping-DNA sequences of the organism in question are compared against a karyotype that specifically looks at restriction sites found within the DNA to correctly order the DNA sequences on a chromosome. This methodology gives very detailed haplotype information and allows for the detection of sequence variations across an entire genome optical mapping (Pallavi)

ortholog-different DNA sequences that look very similar, but have no evolutionary relationship (Lecture, Pallavi)

oxidoreductase - an enzyme that catalyzes redox reactions by transferring electrons from one molecule (the reductant) to another (the oxidant) [12] (Nick)

P

paralog-identical DNA sequences within a species (Lecture, Pallavi)

phylogenetic tree- a diagram showing the evolutionary relationships between biological species or other entities believed to have a common ancestor [13] (Nick)

plastid - major organelles in plants or algae (Samantha)

proteome - entire set of proteins expressed by a genome, cell, tissue, or organism. It may refer to expressed proteins under certain conditions (Samantha)

psuedogenes-A sequence of DNA that looks like a gene, but most likely contains many stop codons. It may have evolved away from a real gene or a paralog might have taken its place (Lecture, Pallavi)

Q

R

rDNA-These are DNA sequences that encode for ribosomal RNA. Note that rDNA can also stand for recombinant DNA. (rDNA Pallavi)

retrotransposons - RNA transcribed back into DNA and added into the genome (Samantha)

S

Serovar-a subdivision of a species based on the characteristics of their cell surface antigens (serovar Pallavi)
Shine-Dalgarno sequence - A ribosomal binding site on an mRNA, usually a sequence of six base pairs about six or seven base pairs upstream of the start codon. An anti-Shine-Dalgarno sequence exists on the rRNA in the small subunit of the ribosome; when the two sequences align, the mRNA is lined up and prepared for transcription. (Lecture and Wikipedia article, Laura)

Note: The Shine-Dalgarno consensus sequence for our genome is TAGGAGG.

T

transposons / transposable elements - DNA sequences that can move around to different positions in a single cell's genome. Transposons can cause mutations and change the length of the genome. (Samantha)
Transposon Mutagenesis-a procedure in which a transposon is inserted into a gene, which inactivates the gene and can lead to the discovery of the phenotype associated with this gene (transposon mutagenesis Pallavi)

U

V

W

whole genome shotgun sequencing - a method of sequencing where DNA is cut into small pieces and cloned into vectors, then both ends of every vector are sequenced in about 500 bps to form mate pairs. Mate pairs rarely overlap, but are used to reassemble the sequence using software. (Samantha)

X

Y

Z

This is a list of the student-created tutorials: