Lab Exam 2 Flashcards
memorize
mitosis is part of the
cell cycle
mitosis generates
two genetically identical cells
mitosis occurs when an organism
grows or must replace old cells
meiosis only occurs in ____ organisms
sexually reproducing
meiosis cell division
diploid chromosome number is reduced by half -> haploid chromosomes
parts of interphase
G1, S, G2
G1 phase
“gap 1” - cell grows in size, undergoes normal metabolic activity
S phase
synthesis - DNA gets synthesized (replicated)
G2 phase
“gap 2” - cell prepares for cell division
M phase
mitosis (cell division)
stages of DNA distribution
duplication, alignment, separation, cytokinesis
products of DNA duplication
2 identical sister chromatids created
alignment
chromosomes line up in the cell’s center (in metaphase)
separation
sister chromatids are pulled apart to opposite ends of the cell (in anaphase)
cytokinesis
actin filaments create cleavage furrow in the cell membrane
forms 2 identical daughter cells
not a stage of mitosis
prophase
chromosomes condense and become visible
nuclear envelope breaks down
spindle fibers start to form at opposite poles
spindle fibers
structure of microtubules that separate chromosomes by pulling them apart to opposite ends of the cell
actin filaments
thin protein strands
help cell keep its shape and move
plant cell cytokinesis
formation of cell plate to divide the cell
cell plate formation
vesicles from Golgi apparatus are delivered to the middle of the plant cell and fuse to create a new cell wall
chromosome pairing in meiosis
somatic cells have pairs of homologous chromosomes
homologous chromosomes
carry information about the same traits but can have genetic variation in alleles
somatic cells
diploid (2n)
1 chromosome from each pair from mother and 1 from father
gametes
haploid (n)
reproductive cells (sperm and eggs) containing one chromosome of each type (not 2)
meiosis I
homologous chromosomes pair up and then separate
diploid -> haploid
meiosis II
sister chromatids separate
produces 4 haploid cells
outcome of meiosis
4 genetically unique haploid gametes
where does mitosis occur
all over the body
allows for growth, repair, maintenance of tissues and organs
where does meiosis occur
only in gonads (testes and ovaries) for sexual reproduction
G0 phase
cells that don’t replicate stay in this phase
karyokinesis
another word for mitosis
when are centrioles replicated?
before mitosis begins - during S phase
cytokinesis begins during
late anaphase
checkpoint 1 - after G3
assessing QUALITY of DNA
checkpoint 2 - after G2
assessing QUANTITY of DNA
checkpoint 3 - metaphase
make sure all chromosomes are lined up in the middle to prevent non-disjunction
mitosis # of divisions
1
meiosis # of divisions
2
does mitosis produce genetic diversity
no
does meiosis produce genetic diversity
yes
spermatogenesis takes place in the
testes
how long does the sperm cycle last
entire male adult life
each cycle of meiosis forms ___ sperm
4
oogenesis takes place in the
ovary
each cycle of meiosis forms ___ egg(s)
1
how long does oogenesis take place
it ends later in life and has long periods of interruptions
spermatogenesis
germ cell -> stem cells -> mitosis -> spermatogonia -> mitosis -> primary spermocytes -> meiosis I -> secondary spermocytes -> meiosis II -> spermatids -> differentiation into sperm
where are the stem cells in testes situated
near the outer edges of the seminiferous tubules - where there is a concentric organization of the steps of spermatogenesis
cell movement during spermatogenesis
tubule periphary -> lumen as they turn from the primary spermocyte into spermatids
mature cells are released into the lumen
sperm cells become motile when
they pass from the lumen to the epididymus
sperm cell head
houses a haploid nucleus capped with the acrosome
acrosome
houses enzymes which help with egg penetration
whats in the sperm cell behind the head
lots of mitochondria to produce ATP to power movement with the flagellum (tail)
when does oogenesis begin
during fetal intrauterine development
process of oogenesis
primordial stem cells -> oogonia -> mitosis -> meiosis (arrested at prophase I) -> puberty hormone FSH -> meiosis resumes -> secondary oocyte and cell-polar body -> meiosis II (arrested at metaphase II) -> ovulation hormone LH -> secondary oocyte moves from follicle to fallopian tubes -> sperm penetrates oocyte -> meiosis II resumes -> ovum (egg)
haploid nuclei of sperm and ovum fuse to form
diploid zygote
what happened to cells left over from the ruptured follicle on oogenesis
develop into the corpus luteum - establishes and maintains pregnancy
(degenerates if no fertilization)
If an organism has a diploid number of 16, how many chromatids are visible at the end of mitotic prophase?
32
bioinformatics definition
the computational analysis of genomic,
transcriptomic, and proteomic sequences identified in biological
studies.
BLAST stands for
Basic Local Alignment Search Tool
what does blast do
looks for the best whole sequence alignment
Pfam
protein family analysis - looks for relevant protein families based on the functional domains in the sequence
body mapping
provides info on the function of a gene/protein in a specific organism
BLAST matches will be
to the gene of a particular species
alignment of query to database
- compares your sequence (query) to sequences in a large
database - uses pairwise comparison, checking one match at a time
(between query and database sequence) - employs quick methods (heuristics) for efficiency with large databases
query sequence is usually _____ than the database
smaller - 1k nucleotides vs several billion
drosophila are used as a model organism because
- short lifespan (2 weeks)
- easy to breed
- inexpensive
- large # offspring
drosophila research can contribute to the field of
regenerative medicine
shape of females vs males
males have a rounded caudal end
females have a sharp caudal end
size of females vs males
females are larger and longer
color of females vs males
males have more black in their caudal end
typical fruit fly appearance
yellow body with black stripes
round red eyes
normal wings
sex combs
found on front legs of males
dumpy
small round wings
vestigial
crumpled up wings
apterous
no wings
bar
bar shaped eyes
ebony
dark/black body
sepia
brownish eyes
antennapedia
extra legs where antenna should be
white
white eyes
stripes on male vs female
males have fewer thick stripes
females have more thin stripes
chi squared value is greater than the critical value
reject the null hypothesis - findings are statistically significant
null hypothesis in this context
traits that are being studied follow Mendelian patterns of inheritance
circle on a pedigree
female
square on a pedigree
male
filled in shape
individual displays relevant trait
crossed out shape
individual is dead
autosomal dominant
- trait appears in every generation
- Affected individuals have at least one affected parent.
- Both males and females are equally affected
- affected individuals have a 50% chance of passing it on
autosomal recessive
- may skip generations
- 2 unaffected carrier parents can have affected children
- males and females are equally affected
X-linked dominant
- appears in every generation
- affected fathers pass it to all daughters and no sons
- both genders can be affected - heterozygous females may show fewer symptoms
X-linked recessive
- more common in males
- affected males often have carrier mothers
- affected mothers pass it to all sons
- can skip generations when females are carriers but not affected
evolution
change in frequencies in the alleles in the gene pool of a population
evolution will not occur in a population if:
- mutation is not occurring
- migration in and out is not occurring
- infinitely large population
- natural selection is not occurring
- random mating (all members breed and all produce same # offspring)
chi squared formula
x^2 = sum of (O-E)^2 / E
degree of freedom
phenotypes - 1
hardy weinberg equation
p2 + 2pq + q2 = 1
determine # of possible alignments
(2^2n) / (√pi * 2) when n = number of base pairs
pairwise comparison
the query sequence is compared to each sequence in a database one at a time
dealing with large database size
using heuristic methods to find matches
global alignment
tries to align 2 entire sequences from start to finish
difficult because sequences may be different lengths or have different starting points
local alignment
focus on smaller sections in the sequence using a specific “word” size
ex. size 5 - look for matching pairs of 5 bases
scoring alignments
assign costs to different types of the differences between sequences
determines the quality of the alignment
i.e. if something “loses” a point for every difference in the sequence, and the number of points lost is determined by the type of difference
transition
nucleotide mutation between 2 of the same type (ex. purine swaps with purine)
transversion
change from one nucleotide type to the other
indels
insertions/deletions - adding or removing bases from the sequence
inversion
reversing a segment of the sequence
seed
point where alignment starts - short, exact match found between two sequences
extending the seed
the alignment is extended in both directions (left and right) to form a larger match without any gaps
this creates a longer, continuous segment where the sequences are similar
gapped alignment
created after match is established
the alignment can now include some mismatches and gaps (insertions or deletions) to better fit the sequences together
blastn
nucleotide-nucleotide comparison
blastp
protein-protein comparison
blastn and blastp are used to
identify an unknown sequence
traditional BLAST searches
blastx, tblastx, blastn
take a nucleotide sequence, generates the six possible translation products (based on the six open reading
frames), and performs BLAST protein-protein alignments
used to identify the protein
corresponding to a gene sequence, or the gene sequence corresponding to a protein
PSI BLAST
position-specific iterative
more sensitive version of blastp
takes the best protein-protein alignments, determines the most conserved amino acids between them,
and performs additional searches for other proteins containing those conserved amino acids
Used to identify distantly related proteins
megablast
used when comparing a large set of sequences to another large database of sequences
- optimized version of BLAST to allow fast searching with large sets of sequences - by increasing size of “words” it searches for
Pfam
databases containing functional domains conserved across protein families
distantly related proteins will
not have a lot of matching amino acids
vital regions of the protein are
highly conserved
ex. beta-galactosidase protein has small catalytic site to break down sugars - highly conserved across species
Pfam is different from blast because
pfam does not use a local alignment approach
pfam is more sensitive and can find conserved domains even when proteins are distantly related
body mapping can answer these questions
Where is this gene expressed?
What tissues require this protein to function?
In what subcellular compartment is it located?
In which pathways and protein interactions does it take part?
Are there any diseases associated with this protein?
how to answer questions about proteins
the human protein reference database
