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Spring Semester > Genetics Exam 2 > Flashcards

Genetics Exam 2 Flashcards

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
Q

Restriction Fragment Length Polymorphism (RFLPs)

A

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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26
Q

restriction enzymes

A

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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27
Q

Allele-specific oligonucleotides (ASOs)

A

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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28
Q

cell cycle

A 
Go phase 
G1
S phase 
G2
M phase 
G1 & repeat
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29
Q

M phase

A

Prophase
Metaphase
Anaphase
Telophase

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30
Q

Mitosis

A

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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31
Q

Prophase

A

chromosomes condense into structures we see (already duplicated)

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32
Q

Metaphase

A

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

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33
Q

Anaphase

A

sister chromatids separate

34
Q

Meiosis

A

occurs only in germ cells (cells that make sperm & egg)

same stages as Meiosis but undergoes metaphase and anaphase twice)

35
Q

Goals of meiosis

A

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
Q

Prophase 1

A

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
Q

Metaphase meiosis 1

A

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

38
Q

Anaphase 1

A

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

39
Q

Germ Cells

A

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

40
Q

centromere

A

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

41
Q

homologous chromosomes

A

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

42
Q

sister chromatids

A

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

43
Q

true breeding organisms

A

only produce one trait over several generations

44
Q

P, F1, F2

A

Parental, 1st Filial, 2nd Filial

45
Q

Law of Independent Assortment

A

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
Q

Homozygosity

A

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

47
Q

Heterozygosity

A

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

48
Q

gene

A

a unit of heredity

49
Q

allele

A

alternate forms of a single gene

50
Q

principle of segregation

A

alleles segregate during gamete formation b/c of meiosis

51
Q

product rule

A

probability of two independent events occurring together (and)

52
Q

addition rule

A

probability of mutually exclusive events (or)

53
Q

Chi Square statistical test

A

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

54
Q

chi square conclusions

A

P>0.50 accept hypothesis, differences are due to chance

p

55
Q

chromosomal sex determination

A

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
Q

non chromosomal sex determination

A

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
Q

Barr Body

A

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
Q

Autosomal dominant inheritance

A

alleles show a vertical pattern to inheritance

an infected individual has at least one affected parent –> there are no carriers

59
Q

Autosomal recessive inheritance

A

alleles show a horizontal pattern of inheritance

affected individuals may have affected siblings, but parents need not be affected (they must be carriers)

60
Q

X-linked recessive inheritance

A

females are usually no affected unless father is affected and mother is carrier
each male can be traced back to carrier mother

61
Q

X-linked dominant inheritance

A

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
Q

three types of chromosome problems

A
  1. chromosome rearrangement (duplication)
  2. aneuploidy (trisomy)
  3. polyploidy
63
Q

chromosome rearrangement

A

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
Q

aneuploidy

A

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

65
Q

Nondisjunction in meiosis 1

A

fail to separate homologous chromosomes

-only one chromosome undergoes the nondisjunction

66
Q

Nondisjunction in meiosis 2

A

fail to separate sister chromatids

67
Q

Independent assortment

A

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

68
Q

genetic linkage

A

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

69
Q

haplotype

A

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

70
Q

linked genes do not assort independently

A

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
Q

recombination

A

only one sister of each homologous recombines

72
Q

recombination frequency correlates with the distance

A

between genes on the chromosome

73
Q

genes close together on chromosome

A

will be inherited together

  • more parental types
  • few recombinant types
74
Q

genes far aprat on chromosome

A

‘linkage’ tends to break

  • fewer parental types
  • more recombinant types
75
Q

incomplete dominance

A

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

76
Q

codominance

A

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

77
Q

incomplete penetrance

A

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

78
Q

variable expressivity

A

degree or intensity of a phenotype

single tumor or multiple tumors

79
Q

genetic heterogeneity (heterogenous trait)

A

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

80
Q

lethal gene

A

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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