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Spring Semester > Genetics Exam 2 > Flashcards

Genetics Exam 2 Flashcards

(80 cards)

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1
Q

Sanger Sequencing

A

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

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2
Q

dideoxynucleotides

A

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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3
Q

Next generation sequencing

A

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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4
Q

contigs

A

fragments aligned based on identical DNA sequences

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5
Q

open reading frame

A

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

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6
Q

Microarray experiment

A

microscopic DNA spots collection attached to a solid surface&raquo_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

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7
Q

what molecule are you directly comparing in this microarray experiment?

A

mRNA

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8
Q

green spot

A

gene expressed in healthy cells (transcribed)

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9
Q

black spot

A

gene not expressed in healthy cells

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10
Q

yellow spot

A

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

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11
Q

red spot

A

gene is overexpressed in cancer cells

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12
Q

microarray steps

A
  • 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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13
Q

homology

A

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

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14
Q

similiarity

A

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

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15
Q

BLAST

A

Basic Local Alignment Search Tool

a software application for comparing sequence data (DNA, RNA, Protein) to search for sequence similarities

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16
Q

blast input

A

a sequence is broken into “words” & “similar words”

this can bed done with DNA or animo acid sequence

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17
Q

e vaue

A

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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18
Q

blast output

A 
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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19
Q

motifs

A

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

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20
Q

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

A
  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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21
Q

Short Tandem Repeats (STRs / micro satellites)

A

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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22
Q

Variable Number Tandem Repeats (VNTRs/mini satellites)

A
  • 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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23
Q

Single Nucleotide Polymorphisms (SNPs)

A

-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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24
Q

probe

A

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

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25
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
26
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
27
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
28
cell cycle
``` Go phase G1 S phase G2 M phase G1 & repeat ```
29
M phase
Prophase Metaphase Anaphase Telophase
30
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
31
Prophase
chromosomes condense into structures we see (already duplicated)
32
Metaphase
replicated chromosomes line up along the middle of the cell (metaphase plate)
33
Anaphase
sister chromatids separate
34
Meiosis
occurs only in germ cells (cells that make sperm & egg) | same stages as Meiosis but undergoes metaphase and anaphase twice)
35
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
36
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
37
Metaphase meiosis 1
two possibilities for any set of homologous chromosomes that result in different gametes
38
Anaphase 1
separation, each cell has one replicated copy of each chromosome and each cell goes through Anaphase and Metaphase a 2nd time
39
Germ Cells
B/c the alleles on each homologous chromosomes are different & bc of recombination each germ cell is unique
40
centromere
the attachment point of the replicated chromosomes & the part that gets pulled when chromosomes separate
41
homologous chromosomes
chromosomes that synapse or pair during meiosis and that are identical with respect to their genetic loci and centromere placement
42
sister chromatids
either of two identical copies (chromatids) formed by replication of a single chromosome
43
true breeding organisms
only produce one trait over several generations
44
P, F1, F2
Parental, 1st Filial, 2nd Filial
45
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
46
Homozygosity
produces only one type of gamete AA or aa Refers to a condition where both alleles of a gene pair are the same
47
Heterozygosity
produces 2^n types of gametes Aa refers to the condition where members of a gene pair are different
48
gene
a unit of heredity
49
allele
alternate forms of a single gene
50
principle of segregation
alleles segregate during gamete formation b/c of meiosis
51
product rule
probability of two independent events occurring together (and)
52
addition rule
probability of mutually exclusive events (or)
53
Chi Square statistical test
calculates the probability that the deviation b/w observed data and expected results is due to chance alone
54
chi square conclusions
P>0.50 accept hypothesis, differences are due to chance | p
55
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
56
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
57
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
58
Autosomal dominant inheritance
alleles show a vertical pattern to inheritance | an infected individual has at least one affected parent --> there are no carriers
59
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)
60
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
61
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
62
three types of chromosome problems
1. chromosome rearrangement (duplication) 2. aneuploidy (trisomy) 3. polyploidy
63
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
64
aneuploidy
incorrect number of copies of a chromosome (trisomy of chromosome 21 --> downs syndrome) can also be a monosomy (single chromosome)
65
Nondisjunction in meiosis 1
fail to separate homologous chromosomes | -only one chromosome undergoes the nondisjunction
66
Nondisjunction in meiosis 2
fail to separate sister chromatids
67
Independent assortment
in metaphase of meiosis 1 each homologous pair aligns at the plate independently of all other pairs equal probability of each
68
genetic linkage
alleles of genes that are close together on the same chromosome tend to be inherited together ("linked")
69
haplotype
a set of closely linked genetic markers (could be alleles of genes, could be noncoding sequences) present on one chromosome
70
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
71
recombination
only one sister of each homologous recombines
72
recombination frequency correlates with the distance
between genes on the chromosome
73
genes close together on chromosome
will be inherited together - more parental types - few recombinant types
74
genes far aprat on chromosome
'linkage' tends to break - fewer parental types - more recombinant types
75
incomplete dominance
the dominant allele isn't completely expressed when the recessive allele is also present (blending)
76
codominance
the two alleles work together & both are expressed (speckled chicken)
77
incomplete penetrance
% of individuals with the genotype that show the expected genotype (having the genotype but not expressing the phenotype)
78
variable expressivity
degree or intensity of a phenotype | single tumor or multiple tumors
79
genetic heterogeneity (heterogenous trait)
a trait that can arise from a mutation in more than one gene
80
lethal gene
a gene whose expression results in premature death of the organism at the same stage of its life cycle

Spring Semester (13 decks)

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