Genetics Exam 2 Flashcards
Sanger Sequencing
a short primer is binded next to the region of interest. In presence of the four nucleotides, the polymerase will extend the primer by adding on the complementary nucleotides (dNTPs)»_space; high concentration to stop it»_space; (ddNTPs) dideoxynucleotides that has a fluorescent molecule/marker
1st generation sequencing
dideoxynucleotides
ddATP, ddTTP, ddGTP, ddCTP
cause chain termination because they lack a free 3’ hydroxyl group so no new nucleotides can be added (remove oxygen)
Next generation sequencing
faster sequencing & allow huge number of DNA fragments to be simultaneously sequenced -it sequences shorter pieces of DNA but more accurate
contigs
fragments aligned based on identical DNA sequences
open reading frame
simplest way to find a gene b/w the start codon and the stop codon in a DNA sequence
Microarray experiment
microscopic DNA spots collection attached to a solid surface»_space; used to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of the genome (used in tumor profiling)
comparing gene expression levels between healthy cells and cancer cells –each spot represents one gene
what molecule are you directly comparing in this microarray experiment?
mRNA
green spot
gene expressed in healthy cells (transcribed)
black spot
gene not expressed in healthy cells
yellow spot
gene is expressed at equal levels in healthy cells and cancer cells
red spot
gene is overexpressed in cancer cells
microarray steps
- bind DNA to spots on microarray
- isolate mRNA from tissue type of interest
- generate cDNAs (complementary) from the mRNAs, in which the pieces are labeled with green or red fluorescence depending on which tissue type they came from
- bind the cDNAs to the microarray: genes that are expressed in the original tissue type will be represented by the cDNAs and will bind to the spots on the microarray
homology
derived from the same ancestral gene or ancestral species (a yes/no condition)
similiarity
sequences share some of the same bases or amino acids (a percent condition like 80% similarity)
BLAST
Basic Local Alignment Search Tool
a software application for comparing sequence data (DNA, RNA, Protein) to search for sequence similarities
blast input
a sequence is broken into “words” & “similar words”
this can bed done with DNA or animo acid sequence
e vaue
expectation value (lower E value, the more similar, less likely to occur by chance)
- a measure of the alignment of two sequences
- the likelihood that this match could have occurred by chance
blast output
center row ("consensus"):
letter=sequence is identical
\+= amino acids are similar (hydrophobic, charge, size)
a space = sequences are different
---- = one sequence is longer (has amino acids the other doesn't)motifs
regions of proteins that perform important functional roles & are likely to be found in homologous proteins across species
Four types of variation in the genome that comes from repetitive sequences (& are easy to test for)
- Short Tandem Repeats (STRs)
- Variable Number Tandem Repeats (VNTRs)
- Single Nucleotide Polymorphisms (SNPs)
- Restriction Fragment Length Polymorphisms (RFLPs)
Short Tandem Repeats (STRs / micro satellites)
short repeats, 2-9 base pairs, repeated 7-40 times
all STR sequences are in non-gene regions
-hundreds of STR loci are present in the human genome: 13 specific loci are used for most DNA profiling analysis
Variable Number Tandem Repeats (VNTRs/mini satellites)
- located in noncoding regions
- DNA sequences b/w 15 and 100 bp long
- # of repeats at VNTR locus varies in individuals
- isolated VNTR regions of DNA from individual are separated on gel, where alleles can be determined based on size of repeat
- there is VNTR based fingerprinting
Single Nucleotide Polymorphisms (SNPs)
-single nucleotide differences between two DNA molecules
-SNPs occur randomly throughout the genome & on mtDNA about every 500 to 1000 nucleotides
–millions of loci on the human genome can be used for profiling
*PCR amplify region of interest
*Determine whether allele 1 or allele 2 is found in any individual by generating a “probe”
bind probe to DNA isolated from person
probe
a sequence of DNA that is complementary to sequence of interest
-used in SNPs
Restriction Fragment Length Polymorphism (RFLPs)
based on restriction enzymes
If a gene contains a restriction enzyme site in a location where there are known single base mutations, a restriction digest will generate different sized fragments of DNA
SNP must occur within restriction enzyme recognition sequence
restriction enzymes
proteins from bacteria that cut both strands of DNA in a specific location determined by sequence
-produced by bacteria as a defense mechanism against bacteriophage
-enzyme cleaves both strands of DNA at the restriction sites
most cut at “palindrome” sites: CAATTG or GTTAAC
DNA pieces can be separated on a gel
Allele-specific oligonucleotides (ASOs)
short single-stranded fragments of DNA that are specifically generated to be used as probes to identify alleles that differ by a single-oligonucleotide (SNPs)
- DNA from individual is placed in a spot on a filter
- probes are then used to bind to the DNA
- the probe will bind if it is an exact match
cell cycle
Go phase G1 S phase G2 M phase G1 & repeat
M phase
Prophase
Metaphase
Anaphase
Telophase
Mitosis
occurs in somatic body cells
-somatic cells are exact duplicates of each other
-fidelity of replication & separation is critical
The goal is two diploid cells with 2 chromosomes copies of each chromosome
Prophase
chromosomes condense into structures we see (already duplicated)
Metaphase
replicated chromosomes line up along the middle of the cell (metaphase plate)
Anaphase
sister chromatids separate
Meiosis
occurs only in germ cells (cells that make sperm & egg)
same stages as Meiosis but undergoes metaphase and anaphase twice)
Goals of meiosis
begin with a normal cell with 2 copies of each chromosome and end with a cell that has half the genetic content (1 copy of each chromosome)
Part 1: separate homologous chromosomes into two cells
Part 2: separate the sister chromatids in each of the two cells for a final count of 4 cells
Prophase 1
homologous chromosomes can exchange material (recombination) crossing over
- occurs anywhere along the chromosome
- occurs multiple times on each set of h chromosomes
- results in exchange of DNA sequence between homologous chromosomes
Metaphase meiosis 1
two possibilities for any set of homologous chromosomes that result in different gametes
Anaphase 1
separation, each cell has one replicated copy of each chromosome and each cell goes through Anaphase and Metaphase a 2nd time
Germ Cells
B/c the alleles on each homologous chromosomes are different & bc of recombination each germ cell is unique
centromere
the attachment point of the replicated chromosomes & the part that gets pulled when chromosomes separate
homologous chromosomes
chromosomes that synapse or pair during meiosis and that are identical with respect to their genetic loci and centromere placement
sister chromatids
either of two identical copies (chromatids) formed by replication of a single chromosome
true breeding organisms
only produce one trait over several generations
P, F1, F2
Parental, 1st Filial, 2nd Filial
Law of Independent Assortment
during gamete formation, the segregation of any pair of hereditary determinants is independent of the segregation of other pairs - gametes reunite randomly to generate offspring
-All possible gamete combination are formed with equal probability –» alleles assort independently into genetics
Homozygosity
produces only one type of gamete
AA or aa
Refers to a condition where both alleles of a gene pair are the same
Heterozygosity
produces 2^n types of gametes
Aa
refers to the condition where members of a gene pair are different
gene
a unit of heredity
allele
alternate forms of a single gene
principle of segregation
alleles segregate during gamete formation b/c of meiosis
product rule
probability of two independent events occurring together (and)
addition rule
probability of mutually exclusive events (or)
Chi Square statistical test
calculates the probability that the deviation b/w observed data and expected results is due to chance alone
chi square conclusions
P>0.50 accept hypothesis, differences are due to chance
p
chromosomal sex determination
homogametic: two of the same sex chromosome XX
heterogametic: two different sex chromosomes XY
dosage of the X can be seen in some invertebrates
non chromosomal sex determination
environmental; scattered genes (not on a designated chromosome)
-the situation (environment, not genetics) defines the hormones being secreted and this defines the sex of the animal
Barr Body
if a mammal has more than one X chromosome, most of one of the X chromosomes is inactivated in each cell in the early embryo
Autosomal dominant inheritance
alleles show a vertical pattern to inheritance
an infected individual has at least one affected parent –> there are no carriers
Autosomal recessive inheritance
alleles show a horizontal pattern of inheritance
affected individuals may have affected siblings, but parents need not be affected (they must be carriers)
X-linked recessive inheritance
females are usually no affected unless father is affected and mother is carrier
each male can be traced back to carrier mother
X-linked dominant inheritance
both males and females can be affected
affected father will have all affected daughters but no sons
Affected father will have affected daughters and sons
three types of chromosome problems
- chromosome rearrangement (duplication)
- aneuploidy (trisomy)
- polyploidy
chromosome rearrangement
duplications & deletions can occur from unequal crossing over during meiosis –> unbalanced gene dosage
inversions and translocations can occur due to chromosomal breaks during mitosis & meiosis all genes are present
aneuploidy
incorrect number of copies of a chromosome
(trisomy of chromosome 21 –> downs syndrome)
can also be a monosomy (single chromosome)
Nondisjunction in meiosis 1
fail to separate homologous chromosomes
-only one chromosome undergoes the nondisjunction
Nondisjunction in meiosis 2
fail to separate sister chromatids
Independent assortment
in metaphase of meiosis 1 each homologous pair aligns at the plate independently of all other pairs
equal probability of each
genetic linkage
alleles of genes that are close together on the same chromosome tend to be inherited together (“linked”)
haplotype
a set of closely linked genetic markers (could be alleles of genes, could be noncoding sequences) present on one chromosome
linked genes do not assort independently
no gametes have Ab or aB genotype because genes are completely linked
only AB or ab haplotype could be contributed to the next generation
recombination
only one sister of each homologous recombines
recombination frequency correlates with the distance
between genes on the chromosome
genes close together on chromosome
will be inherited together
- more parental types
- few recombinant types
genes far aprat on chromosome
‘linkage’ tends to break
- fewer parental types
- more recombinant types
incomplete dominance
the dominant allele isn’t completely expressed when the recessive allele is also present (blending)
codominance
the two alleles work together & both are expressed (speckled chicken)
incomplete penetrance
% of individuals with the genotype that show the expected genotype (having the genotype but not expressing the phenotype)
variable expressivity
degree or intensity of a phenotype
single tumor or multiple tumors
genetic heterogeneity (heterogenous trait)
a trait that can arise from a mutation in more than one gene
lethal gene
a gene whose expression results in premature death of the organism at the same stage of its life cycle
