Genetics Exam 2 Flashcards Preview

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Flashcards in Genetics Exam 2 Deck (80):
1

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) >> high concentration to stop it >> (ddNTPs) dideoxynucleotides that has a fluorescent molecule/marker
1st generation sequencing

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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)

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Next generation sequencing

faster sequencing & allow huge number of DNA fragments to be simultaneously sequenced -it sequences shorter pieces of DNA but more accurate

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contigs

fragments aligned based on identical DNA sequences

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open reading frame

simplest way to find a gene b/w the start codon and the stop codon in a DNA sequence

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Microarray experiment

microscopic DNA spots collection attached to a solid surface >> 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

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what molecule are you directly comparing in this microarray experiment?

mRNA

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green spot

gene expressed in healthy cells (transcribed)

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black spot

gene not expressed in healthy cells

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yellow spot

gene is expressed at equal levels in healthy cells and cancer cells

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red spot

gene is overexpressed in cancer cells

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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

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homology

derived from the same ancestral gene or ancestral species (a yes/no condition)

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similiarity

sequences share some of the same bases or amino acids (a percent condition like 80% similarity)

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BLAST

Basic Local Alignment Search Tool
a software application for comparing sequence data (DNA, RNA, Protein) to search for sequence similarities

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blast input

a sequence is broken into "words" & "similar words"
this can bed done with DNA or animo acid sequence

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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

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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)

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motifs

regions of proteins that perform important functional roles & are likely to be found in homologous proteins across species

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Four types of variation in the genome that comes from repetitive sequences (& are easy to test for)

1. Short Tandem Repeats (STRs)
2. Variable Number Tandem Repeats (VNTRs)
3. Single Nucleotide Polymorphisms (SNPs)
4. Restriction Fragment Length Polymorphisms (RFLPs)

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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

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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

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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

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probe

a sequence of DNA that is complementary to sequence of interest
-used in SNPs

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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

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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

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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

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cell cycle

Go phase
G1
S phase
G2
M phase
G1 & repeat

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M phase

Prophase
Metaphase
Anaphase
Telophase

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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

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Prophase

chromosomes condense into structures we see (already duplicated)

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Metaphase

replicated chromosomes line up along the middle of the cell (metaphase plate)

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Anaphase

sister chromatids separate

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Meiosis

occurs only in germ cells (cells that make sperm & egg)
same stages as Meiosis but undergoes metaphase and anaphase twice)

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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

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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

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Metaphase meiosis 1

two possibilities for any set of homologous chromosomes that result in different gametes

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Anaphase 1

separation, each cell has one replicated copy of each chromosome and each cell goes through Anaphase and Metaphase a 2nd time

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Germ Cells

B/c the alleles on each homologous chromosomes are different & bc of recombination each germ cell is unique

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centromere

the attachment point of the replicated chromosomes & the part that gets pulled when chromosomes separate

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homologous chromosomes

chromosomes that synapse or pair during meiosis and that are identical with respect to their genetic loci and centromere placement

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sister chromatids

either of two identical copies (chromatids) formed by replication of a single chromosome

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true breeding organisms

only produce one trait over several generations

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P, F1, F2

Parental, 1st Filial, 2nd Filial

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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

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Homozygosity

produces only one type of gamete
AA or aa
Refers to a condition where both alleles of a gene pair are the same

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Heterozygosity

produces 2^n types of gametes
Aa
refers to the condition where members of a gene pair are different

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gene

a unit of heredity

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allele

alternate forms of a single gene

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principle of segregation

alleles segregate during gamete formation b/c of meiosis

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product rule

probability of two independent events occurring together (and)

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addition rule

probability of mutually exclusive events (or)

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Chi Square statistical test

calculates the probability that the deviation b/w observed data and expected results is due to chance alone

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chi square conclusions

P>0.50 accept hypothesis, differences are due to chance
p

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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

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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

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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

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Autosomal dominant inheritance

alleles show a vertical pattern to inheritance
an infected individual has at least one affected parent --> there are no carriers

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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)

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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

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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

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three types of chromosome problems

1. chromosome rearrangement (duplication)
2. aneuploidy (trisomy)
3. polyploidy

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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

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aneuploidy

incorrect number of copies of a chromosome
(trisomy of chromosome 21 --> downs syndrome)
can also be a monosomy (single chromosome)

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Nondisjunction in meiosis 1

fail to separate homologous chromosomes
-only one chromosome undergoes the nondisjunction

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Nondisjunction in meiosis 2

fail to separate sister chromatids

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Independent assortment

in metaphase of meiosis 1 each homologous pair aligns at the plate independently of all other pairs
equal probability of each

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genetic linkage

alleles of genes that are close together on the same chromosome tend to be inherited together ("linked")

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haplotype

a set of closely linked genetic markers (could be alleles of genes, could be noncoding sequences) present on one chromosome

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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

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recombination

only one sister of each homologous recombines

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recombination frequency correlates with the distance

between genes on the chromosome

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genes close together on chromosome

will be inherited together
-more parental types
-few recombinant types

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genes far aprat on chromosome

'linkage' tends to break
-fewer parental types
-more recombinant types

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incomplete dominance

the dominant allele isn't completely expressed when the recessive allele is also present (blending)

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codominance

the two alleles work together & both are expressed (speckled chicken)

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incomplete penetrance

% of individuals with the genotype that show the expected genotype (having the genotype but not expressing the phenotype)

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variable expressivity

degree or intensity of a phenotype
(single tumor or multiple tumors)

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genetic heterogeneity (heterogenous trait)

a trait that can arise from a mutation in more than one gene

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lethal gene

a gene whose expression results in premature death of the organism at the same stage of its life cycle