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What does Bioinformatics mean?
The application of computational tools to genomic and biological data
What does BLAST stand for?
Basic Local Alignment Search Tool
What is the input in BLAST?
The Query sequence
What is the sequence we compare our input to?
The reference sequence
The reference sequence comes from
A genomic database
What does Blast n look at?
Nucleotide sequences from the DNA
What does Blast p look at?
The protein sequence of amino acids
What do we use for sequence alignment in blast?
The Global Align Tool
What does the global align tool do?
Show the two sequences aligned
What does the CD Search tool do?
Allows you to enter a protein sequence and use the database to find sequence motifs
What type of cells is mitosis active in?
Somatic cells
Mitosis occurs after
Duplication, in the S phase
Mitosis occurs during the
M phase
Mitosis produces cells of
2n ploidy- diploid
G1 and G2 are
Growth phases, occurring before and after S phase
S phase is
Synthesis, when cells replicate their DNA
Meiosis produces
Gametic cells- sperm and egg
Cells produced through meiosis have
Ploidy n- haploid
Crossing over can occur only in
Meiosis
Oogenesis occurs in
The ovaries
Spermatogenesis occurs in
The testes
How many gametes are made in oogenesis?
One, as a result of uneven divisionH
Does oogenesis ever end?
Yes, late in the females lifeD
Does oogenesis have interruptions?
Yes, for long periods of time
Does oogenesis show equal division of the cytoplasm?
No, the cytoplasm splits unevenly
How many mature gametes are produced in spermatogenesis?
Four
Does spermatogenesis ever end?
No, it occurs throughout the males entire life
Does spermatogenesis have interrruptions?
No, it does not have any extended interruptions
Where does most of the cytoplasm end up following oogenesis?
In the secondary oocyte and the ootid
The secondary oocyte comes from
Meiosis I
The ootid comes from
Meisosis II
What makes for a good model organism?
Short life span, easy to breed, easy to control, inexpensive
What are the characteristics of a female drosophila?
Larger overall, pointier caudal end
What are the characteristics of a male drisophila?
Darker caudal end, sex combs
Wild type characteristics of drosophila
Round red eyes, yellow body, black rings around abdomen, normal wings
Wild type image
Dumpy drosophila phenotype
Abnormal wing morphology
Dumpy phenotype image
Vestigial drosophila phenotype
Crumpled wings
Vestigial drosophila image
Bar drosophila phenotype
Abnormal eye morphologyB
Bar drosophila image
Ebony drosophila phenotype
Dark/black body
Ebony drosophila image
Sepia drosophila phenotype
Brownish eyesS
Sepia drosophila image
Antennapedia drosophila phenotype
Legs form where the antennae should be
Antennapedia drosophila image
White drosophila phenotype
White eyes
White drosophila image
What is meant by gene mapping?
Based on the analysis of crossing-over events we can estimate the distance between loci
What is our model organism for gene mapping?
Sordaria
Sordaria produce 8 gamete
Ascospores
When no crossing over occurs, we see phenotype
Of 4 black and 4 brown/orange in a row
8 haploid ascospores exist in one
Ascus (pl. asci)
Roughly 20 asci form one
Perithecium
The phenotype in which no crossing over has occurred is known as
Parent type, First division
When crossing over has occurred, we call this phenotype
Second division
First division segregants are
Non-recombinants
Second division segregants are
Recombinants
Why are recombinants called second-division segregants?
Because the alleles don't segregate until after the second division
Why are non-recombinants called first division segregants?
Because the chromosomes with different alleles separated during the first meiotic division
Linkage is a notable exception to
Independent assortment
Traits physically closer together are
More likely to cross over together
Linked genes are closer,
And are less likely to cross over without one another
Chi squared=
sum of [(obs-ex)^2/ex]
The distance between two loci is calculated by
1/2 * (second division)/(first division + second division)
Once we have determined the distance, we
Multiple by 100, converting to map units
Why do we multiply by 1/2 when calculating distance?
Because crossing over only occurs at 50% of chromosomes
What does a low chi squared value indicate in linkage?
You accept the hypothesis, and find that it is unlikely that the alleles are linkedW
What does a high chi squared value indicate in linkage?
You reject the hypothesis, and it is likely that the alleles are linked to one another
Hardy-Weinberg allows us to calculate
Whether or not evolution is occuring
Evolution is shown in ________, not in _________
Species, individuals
Gene pool frequencies are stable,
But all species should evolve overtime
What is the first assumption made for Hardy-Weinberg to be used?
No random mutations are occuring
What is the second assumption made for Hardy-Weinberg to be used?
No natural selection is occuring
What is the third assumption made for Hardy-Weinberg to be used?
The population is infinitely large
What is the fourth assumption made for Hardy-Weinberg to be used?
Mating is 100% random in the species
What is the fifth assumption made for Hardy-Weinberg to be used?
No individuals are emigrating or immigrating
Why is it important for a population to follow Hardy-Weinbergs five assumptions?
As if any of those are false, they can drive evolution.
What is P in Hardy-Weinberg?
The Dominant allele
P=
AA + (1/2)Aa
What is Q in Hardy-Weinberg?
The recessive allele
Q=
aa + (1/2) Aa
The Hardy-Weinberg Equation is
(P)^2 + 2(PQ) + (Q)^2
P^2 represents
Homozygous dominant
2PQ represents
Heterozygous
Q^2 represents
Homozygous recessive
Mitosis results in
Two identical diploid cells, with ploidy 2n
What occurs in mitotic interphase?
the cell grows and makes a copy of its DNA
What occurs in mitotic prophase?
Chromatin condenses and the two sister chromatids are seen, attached to early mitotic spindles
What occurs in mitotic prometaphase?
The nuclear envelope breaks down and kinetochores attach to the sister chromatids
What occurs in mitotic metaphase?
The cell's chromosomes aline along the center of the cell
What occurs in mitotic telophase and cytokinesis?
The cleavage furrow divides the cell into two seperate cells
When is DNA Duplicated?
During the S phase
What happens after S phase?
G2 phase
What is G2 phase?
A growth phase in which the replicated DNA grows to regular size
What happens after G2 phase?
M phase
What happens in M phase?
Mitosis
What comes after M phase?
G1 phase
Note 
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