Genetics Exam 2: Bioinformatics & Microarray

What is a homolog?

two molecules that have derived from a common ancestor

What is a paralog?

homolog that is present in one species that frequently differ in biological function

What is a ortholog?

homolog that is present in different species that frequently have similar or the same function

What e value represents a homolog?

less then or equal to 10^-3

What is a gap?

generated mathematically by BLAST to increase match

What is an identity?

the occurrence of exactly the same nucleotide or amino acid in the same position in aligned sequences

What is similarity?

sequence similarity takes the approximate matches into account and is meaningful only when such substitutions are scored according to some measure of difference or sameness with conservative or highly probable substitutions assigned more favorable scores than non-consecutive or unlikely ones

What is the simple definition for similarity?

the extent to which nucleotide or protein sequences are related

What is the Blosum-62 substitution matrix?

matrix that scores for each position are derived from observations of the frequencies of substitutions in blocks of local alignments in related proteins

What does the B-62 look for?

searches for homology

Does a higher or lower e value mean more silimarity?

lower

What can computer systems search for?

nucleotide sequences, amino acid sequences, "3D structure", and protein motifs

What does in silico mean?

using computer analysis of large amounts of data

What is an orf?

open reading frame

What does S stand for?

stop codon

How many different reading frames are possible for ribosomes to convert mRNA to proteins?

six

Can you BLAST against your same sequence?

yes

What does a asterisk mean in Clustal alignment?

fully conserved

What does a colon mean in Clustal alignment?

similar residue

What does red mean in boxshade?

conserved

What does black mean in boxshade?

not conserved

What are all sequences in organisms that code for product?

genomics

What searches how pieces in a genome interact that leads to a phenotype?

functional genomics

What is how we accumulate, organize, and apple cell information intentionally?

bioinformatics

What are the two things that we talk about in the G&M project?

the human genome project and ELSI

Does more DNA mean a better organism?

no

What is the name of the crude map?

cytogenic mapping

What is cytogenic mapping determined by?

cytogenics

What is cytogenics?

the study of the genetics of cells, particularly cell chromosomes

What is the less crude form of mapping?

linkage mapping

What type of mapping has to do with the percent of a gene and DNA crossing over?

linkage mapping

If a molecular marker moves, does a gene move?

yes

What can linkage mapping be used for?

determine the distance between DNA sequence and order

What is the most precise form of gene mapping?

physical mapping

How is gene mapping determined?

nucleotide to nucleotide sequencing

What was the goal of the Human Genome Project?

to provide a complete and accurate sequence of the 3 billion DNA base pairs that make up the human genome; fre free

What is a SNP?

single nucleotide polymorphism

What is ELSI?

ethical, legal and social implications of gene therapy

What is diauxic growth?

characterized by two distinct growth phases of an organism; diauxic growth occurs in a medium with several

potential carbon and energy sources; the preferred substrate is consumed first, then a lag ensues while the organism induces enzymes needed to consume the remaining substrate, then growth starts up again

What is a diauxic shift?

glucose is exhausted and cells switch to ethanol utilization

What is the expression of every gene in a cell and organism simultaneously?

microarray

What is a plastic chip infused with sequences in a defined order?

microarray

ISs microarray good for gene expression studies?

yes

What are some applications of microarray?

cell-specific gene expression, gene regulation, elucidation of metabolic pathways, tumor profiling, genetic variation, microbial strain identification, and DNA protein binding

What takes mRNA and turns it into a DNA template and turns it into complete DNA?

reverse transcriptase

Does denatured DNA stick to the column?

yes

Does the desired DNA flow through the column?

yes

What places the DNA into a microarray?

robot

What is used to judge levels of flourescence?

scanning microscopy systems

What does a green spot mean in the diauxic shift?

low gene expression/baseline

What does a red spot mean in the diauxic shift?

high gene expression

What does a yellow spot mean in the diauxic shift?

no change in gene expression

What does a no spot mean in the diauxic shift?

no expression of gene at all

What does a column represent in a microarray?

unique sample/tumor

What does a row represent in a microarray?

expression of one gene

What are some downsides of microarray?

needs sequences genome, low sensitivity for detecting molecules, low levels of molecular specificity, hard to modify

What is a NGS?

next generation sequencing

What are benefits of NGS?

no sequenced genome, sensitive to detecting molecules, increased molecular specificity, decreased signal noise

What is a gene called that can complement itself unless both sets of alleles are homozygous recessive?

gene redundancy

What does gene redundancy imply?

that the dominant phenotype is essential

What is a trait that activities of more than one gene affects an organism's phenotype in an additive manner?

polygenic trait

What is a branch of genomics that looks at the genetics of many interrelated organisms?

population genetics

What is a birth defect where a baby is born with seal limbs?

phocomelia

Is thalidomide bad for babies?

yes