Week 4 Flashcards
dna cloning
allows isolation of dna segment and replicate it independently of original context
can make large quantities, can manipulate, etc
restriction enzymes
recognize and cut dna at specific sequences
cells defense against invading dna
-EcoRI, etc.
recognition sequences of different lengths
ligase
covalently attaches dna segments to each other
vector
dna that has origin of relocation and can accept foreign dna segments
life cycle of virus
virus enters cell, gets replicated, transcribed, then viral particles released from cell
RNA virus—made into dna, can be integrated into host genome, code proteins made (reverse transcriptase)
bacteriophages
viruses that infect bacteria
certain bacteria cannot be infected by these—host restricted
palindromic
same meaning forward or backward
restriction enzymes often palindromic
plasmids
circular dna molecules in bacteria
origin allowing dna replication
often carry resistance genes against antibiotics
joining of two different dna fragments
join complementary staggered ends, used ligase (if from same restriction enzyme)
recombinant dna: prereqs
bacteria produce restriction enzymes that recognize specific DNA sequences
bacteria can contain plasmids
Bacteria can take up foreign dna
Ligase to put together
reverse transcriptase
enzyme isolated from retroviruses
reads mRNA into dna, etc.
Gregor Mendel
priest in Austria, bred pea plants
realized that there is genetic material—ahead of his time, ignored
crossing of peas
yellow seeded peas and green seeded
F1 generation 100% yellow
then self fertilization, 75% yellow
- comes from eggs and sperm having gametes
- green peas recessive (lower case)
Mendel’s first law
law of segregation: each individual receives 2 factors (alleles), one from each parent, and each gives one of these two factors to gametes (germ cells) and thus to next generation
homozygous
if factors are identical (for a trait/gene)
if not, hetero
genotype
genetic constitution of an individual
phenotype
appearance or attributes of an individual
locus
place in the genome that is defined—can be a trait, a specific gene, or a specific nucleotide
position in a chromosome of gene or chromosome marker
- names in human genome assigned by committee, italicized in publications
- can be a specific gene, or a specific base
allele
one of several possible forms of a locus
eg y and Y in the pea case—recessive and dominant alleles
law of independent assortment
Genetic factors are distributed independently
closely linked loci
two loci in same chromosome, same phenotype…
Mendelian
a trait of disease that follows the laws of Mendel
recessive disease (human)
called if the wild type is dominant—i.e. if 2 defective copies are needed to get disease
dominant disease
if inherited through generations, one disease allele is sufficient to cause the disease
additive traits
not all traits are dominant or recessive
examples: height, blood pressure, skin color, risk for depression, diabetes, obesity
genetic marker locus
dna segment with an identifiable physical location on a chromosome and inheritance can be tracked
usually used an indirect way of tracking inheritance pattern if gene that has not yet been identified
mutation
change in some disciplines, disease causing change in others
polymorphism
meaning non-disease-causing change, or change found at a frequency of 1 percent or higher in the population
coming in many different forms
sequence variant
different than what’s in standard database, avoids confusion with mutation vs polymorphism
micro satellite markers
genetic marker: alleles that show high degree of variation and are known to be on specific region of chromosome
length variants of short, simple sequence (also called STRP—short tandem repeat polymorphisms)
can be 4-10 alleles of different length at marker locus
13 of this is enough to identify human
pcr amplifies with flanking primers
single nucleotide polymorphism (snp)
any single base change
Most common in mammals: cpg to tpg
several million snps are already publicly available, there are hundreds of snps for each gene
verified
in locus region (win 2kb of gene including introns)
heterozygosity: fraction of human subjects that are heterozygous
lof mutation/snps
loss of function: nonsense(stop) or splice
coding snps
in the coding part of the mRNA
- synonymous (does not change the amino acid sequence)
- nonsynonymous
linkage
caused by loci being close to each other on a chromosome
genes and genetic markers can be separated by a recombination factor—the prob that in any meiosis, there will be a recombination between them
theta = 0.5 indicated complete lack of linkage, theta = 0 indicates very tight linkage
lod score
probability of this particular family constellation if the marker and diseas elocus are linked, and 10 percent recombination between them
lod score if 3 traditionally the threshold to declare linkage
