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BIOL 2030 > Section 3 - Module 10 > Flashcards

Section 3 - Module 10 Flashcards

1
Q

What can influence eDNA?

A

temperature, pH, oxygen, light, microbes, salinity

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2
Q

eDNA

A

environmental DNA

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3
Q

What is the term for creating new genetic variation?

A

genetic engineering

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4
Q

What is chromosome variation?

A

permanent chromosomal changes, changes can be passed to offspring if they occur in cells that will become gametes (‘germline’ cells)

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5
Q

What are the two general types of chromosomal variations?

A

1) chromosome rearrangement
2) variation in chromosome numbers

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6
Q

What is chromosome rearrangement?

A

Changes in the STRUCTURE of individual chromosomes

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7
Q

What is variation in chromosome numbers?

A

changes in the number of chromosomes. One or more individual chromosomes are added or deleted.

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8
Q

What are the 4 types of chromosomal rearrangements:

A

1) deletion
2) duplication
3) inversion
4) translocation

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9
Q

In deletions where can loss of a segment from a chromosome occur?

A

either internal or terminal

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10
Q

how many breaks arises by terminal-ends breaking off?

A

one break

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11
Q

How many breaks results from internal breaking and rejoining of incorrect ends?

A

two breaks

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12
Q

What is the major effect of chromosomal rearrangement deletions?

A

loss of genetic information (importance depends on what, and how much is lost)

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13
Q

How do detect deletions?

A

deletion loops can be detected during meiosis, also by a variety of molecular methods that detect lower heterozygosity or gene dosage

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14
Q

What are the consequences of deletions?

A

1) loss of DNA sequences
2) phenotypic effect depend on the size and location of deleted sequences
3) deletions that span a centromere result in an acentric chromosome (may be lost during cell division, or be lethal)
4) affect gene dosage

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15
Q

What does deletion along the span of a centromere result in?

A

acentric chromosome

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16
Q

What is an acentric chromosome?

A

A fragment of a chromosome (one of the microscopically visible carriers of the genetic material DNA) that is lacking a centromere (the “waist” of the chromosome essential for the division and the retention of the chromosome in the cell) and so is lost when the cell divides.

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17
Q

How can deletions affect gene dosage?

A

1) when a gene is expressed, the functional protein is normally produced at the correct level or dosage
2) some (not all) genes require two copies for normal of protein production; of one copy is deleted a mutant phenotype can result called haploinsufficiency

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18
Q

Haploinsufficiency

A

The situation that occurs when one copy of a gene is inactivated or deleted and the remaining functional copy of the gene is not adequate to produce the needed gene product to preserve normal function.

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19
Q

Why does chromosome variations matter?

A

genetic disorders

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20
Q

What is Cri du chat cause by?

A

deletion of terminal segment on one chromosome in chromosome 5 pair

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21
Q

What is duplication in chromosomal rearrangements?

A

repetition of a chromosome segment, tandem duplication, single gene or or cluster of genes can be duplicated, nothing has been lost so duplications (especially smaller ones) often have little or no effect on phenotype/viability

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22
Q

What is simplest form of duplication?

A

tandem

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23
Q

Why is duplication important for evolution?

A

extra copies of genes provide raw material for new genes and adaptations

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24
Q

How can duplication cause problems (albeit rare)?

A

excess or unbalanced ‘dosage” of gene products (proteins) resulting from duplications

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25
Q

What percent of human genome consists of duplications?

A

5%

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26
Q

How does duplication occur? (the origins)

A

unequal crossing over of misaligned chromosomes during meiosis generates duplicates (and deletions)

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27
Q

How to detect duplications?

A

in alignment in prophase I of meiosis duplicated chromosome form a loop, also by various molecular methods that detect higher geen dosage

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28
Q

What are the evolutionary consequences of duplication?

A

1) both copies remain the same: redundancy, alter gene dosage could have effect
2) one copy becomes inactive: pseudogene
3) one copy acquires a new function: neofunctionalization, gene families

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29
Q

What is a pseudogene?

A

a segment of DNA that structurally resembles a gene but is not capable of coding for a protein.

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30
Q

Consequences of neofunctionalization

A

source of new genes, creates multigene families (example: globin gene families)

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31
Q

How can gene dosage affect phenotype?

A

amount of protein synthesized is often proportional to the number of gene copies present, so extra genes can lead to excess proteins

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32
Q

Example of how gene dosage can affect phenotype?

A

Bar region in drosophila (X chromosome). More copies leads to fewer eye facets

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33
Q

What is chromosomal rearrangements inversion?

A

two breaks in a chromosome followed by reinsertion in the opposite orientation

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34
Q

What are the two types of inversions?

A

1) pericentric (different site of centromere)
2) paracentric (Same of of centromere)

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35
Q

Peri meaning

A

around

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36
Q

para meaning

A

beside

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37
Q

What are the effect if inversions on phenotypes? (although often there is non)

A

sometimes there is an affect on phenotype, driven by the change in position of the gene(s)

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38
Q

Consequences of inversion?

A

position effects (location matters-sometimes), change in position can later expression

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39
Q

Example of inversion consequences

A

Variegation in Drosophila. Genes in/near chromatin may not be expressed

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40
Q

Inversion consequences for recombination and production of gemetes?

A

suppression of recombination

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41
Q

Inversion consequences if no crossing over occurs?

A

gametes produced are usually because genetic information is not lost or gained

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42
Q

Inversion consequences if crossing over occurs?

A

outside of inverted regions = viable gametes. Withing inverted region = some nonviable games and reduced recombination frequency

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43
Q

What does crossing over look like for paracentric inversion?

A

crossing-over between inverted and non-inverted chromosome results in non viable recombinant gametes because they are missing some genes. In the process acentric chromatid is lost and a dicentric bridge breaks as the two centromeres are pulled apart.

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44
Q

Dicentric chromatid

A

are chromosomes that have two centromeres.

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45
Q

What happens to dicentric chromatid?

A

is pulled apart during anaphase of meiosis I with such force that the chromosome breaks at random positions

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46
Q

What does crossing over withing the pericentric inversion look like?

A

crossing over between inverted and non-inverted chromosome results in nonviable recombinant gametes because genes are missing or present in too many copies. Reduced (observed) recombination frequency, reduced fertility

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47
Q

What is chromosomal rearrangement translocation?

A

Exchange of segments between nonhomologous chromosomes, or to a different region on same chromosome. Can be reciprocal or non-reciprocal

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48
Q

Reciprocal meaning

A

two-way

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49
Q

non-reciprocal meaning

A

one-way

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50
Q

Short-term/immediate consequences of chromosome variations?

A

gene/chromosomes dosage effect including genetic disorders, positions effect, effects on recombination & fertility (including miscarriages)

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51
Q

Long-term/evolutionary consequences of chromosome variations?

A

pseudogenes, neofunctionalization, new adaptations

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52
Q

What are the consequences of reciprocal translocation?

A

since it changes the position of genes, this can alter expression of gene(s) because of association with different proteins, or formation of new gene products (fusion proteins)

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53
Q

Example of reciprocal translocation consequences?

A

‘Philadelphia’ chromosome: fused BCR-ABL gene, 5’ section of BCR fused with most of ABL, protein produced is a fusion that functions improperly - causing chronic myelogenous leukemia (CML) (a rare form of cancer that affects certain types of white blood cells)

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54
Q

What do inversion suppress?

A

recombination

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55
Q

How do inversion suppress renominations?

A

lack of recombination within inversion means that genes within the inversion are free to diverge to produce different adaptations

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56
Q

Example of inversion suppressing recombinations?

A

Ruff inversion: ruff is a European wading sandpiper that has 3 typed of males. Feader and satellite males have a 4.5Mb chromosomal inversion that arose 3.8 million years ago. Faeders came first, later a very rare crossover event restored some the the independent version of the chromosome to the faeder version, creating the satellite version. The inversion is LETHAL in HOMOZYGOUS conditions!!

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57
Q

What are the tree types of European wading sandpiper?

A

1) independent: males display in leks to attract females
2) faeder: males mimic females, sneak copulations
3) Satellite: males look like somewhat drabber version of independent males

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58
Q

What European wading sandpiper has cross 2 inverted?

A

not viable

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59
Q

What European sandpiper has cross two not inverted?

A

‘independent’ male

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60
Q

What European sandpiper has cross of inverted and not inverted?

A

faeder male

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61
Q

T/F. Genes within alternate orientations of inversion can diverge dramatically even though there is no divergence anywhere else in the genome.

A

True

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62
Q

Effect of inside inversion (European sandpiper)

A

large divergence

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63
Q

Effect of outside inversion (European sandpiper)

A

zero divergence

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64
Q

Is there recombination within inversion?

A

No

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65
Q

Chromosomal rearrangements of temperate adaptions and migratory behavior in Atlantic cod?

A

Cod have a large chromosomal inversion, genes inside the inversion influence whether cod are adapted to ‘warmer’ or colder’ water, cod with both orientations of the inversion live off nova scotia and interbreed, because recombination inside the inversion is suppressed the warm and cold versions of the genes do not get scrambled by recombination, several other major inversion in cod influence other traits such as migration.

66
Q

Aneuploidy

A

increase or decrease int he number of individual chromosomes, e.g. trisomy

67
Q

trisomy meaning

A

three copies of a chromosome

68
Q

polyploidy

A

increase in the number of sets of chromosomes, e.g. triploid

69
Q

triploidy meaning

A

three copies of every chromsome

70
Q

‘Ploidy’

A

refers to the total number of chromosomes

71
Q

‘somy’

A

refers to the number of particular chromosomes

72
Q

Nullisomy

A

loss of both members of a pair of homologous chromosomes (2n -2 = 44)

73
Q

Monosomy

A

loss of a single chromosome (2n - 2 = 45)

74
Q

Trisomy

A

gain of a single chromosome (2n +1 = 47)

75
Q

Tetrasomy

A

gain of two homologous chromosomes (2n + 2 = 48)

76
Q

What is nondisjunction?

A

failure of homologous chromosomes or sister chromatids to separate

77
Q

Origins of aneuploidy

A

1) nondisjunction in meiosis or mitosis
2) deletion of a centromere leads to chromosome loss

78
Q

Are trisomy viable?

A

may be viable

79
Q

are monosomy viable?

A

usually not viable, except for sec chromosomes

80
Q

Effect of trisomy 13

A

patau syndrome (1/16000)

81
Q

Effect of trisomy 18

A

Edwards syndrome (1/5000)

82
Q

effect of trisomy 21

A

down syndrome (1/800)

83
Q

effect of monosomy X (XO)

A

turner syndrome (girls)

84
Q

Effect of extra copies of the X chromosome (e.g. XXY - most common, XXXY)

A

Klinefelter syndrome (males)

85
Q

What is the most common abnormality

A

trisomy

86
Q

What is trisomy thought to be the most common cause of?

A

spontaneous abortions or miscarriages

87
Q

In most cases of down syndrome who is contributing to the extra chromosome?

A

The mother approximately 75% of the time

88
Q

What causes most cases of familiar down syndrome?

A

Arise in offspring’s of parent who carry a chromosome that underwent Robertsonian translocation

89
Q

Robertsonian translocation

A

exchange of long arms of non-homologous acrocentric chromosomes

90
Q

What is one of the smallest chromosomes?

A

Chromosome 21

91
Q

What does it mean for a gene to be present as a mosaic?

A

not all cell have it

92
Q

Do plants or animals tolerate aneuploidy better?

A

plants

93
Q

Why do plants tolerate aneuploidy better?

A

usually viable; phenotypes maybe altered and fertility reduced

94
Q

Is it more common for plants or animals to be polyploidy?

A

plants

95
Q

Effect of polyploidy on mammals and birds?

A

not known, but presumably lethal

96
Q

What percent of angiosperms evolved via some form of polyploidy?

A

30-35%

97
Q

What are the two types of polyploidy?

A

1) autopolyploid
2) allopolyploid

98
Q

Autoploid

A

multiples of the same genome

99
Q

Allopolyploid

A

multiples of closely related genomes

100
Q

When can the origins of autopolyploid occur?

A

mitosis or meiosis

101
Q

Nondisjunction of ______ during mitosis in early embryo can produce autotetraploid?

A

ALL chromosomes

102
Q

Diploid gamete + normal gamete =

A

autotriploid (3n)

103
Q

Diploid gamete + diploid gamete =

A

autotetraploid (4n)

104
Q

Effects of autopolyploidy

A

usually sterile (odd-numbered ploidy), most gametes produced are genetically unbalanced

105
Q

What is required to convert sterile hybrid into fertile ‘new’ species?

A

chromosome doubling (hybrid is sterile, unbalanced gametes are nonviable), BUT if entire genomes doubled by mitotic nondisjunction, the fertility problem is fixed

106
Q

Significance of polyploid in agriculture

A

1) cell volume correlated with nuclease volume, correlated with genome size
2) polyploids often have bigger leaves, fruit seeds
3) bread wheat is a polyploid derived from 3 species
* production of larger fruits, production of seedless fruit (sterile)

107
Q

Issues with polyploidy (bananas example)

A

“gros michel” wiped out by “Panama disease” (fusarium) and replaced with resistant cavendish(AAA), but now with new strain if fusarium “tropical race 4” cavendish has no resistance. Not easy to produce new banana types

108
Q

A mutation can either be __

A

rare or common (but ultimate source of all genetic variation)

109
Q

Rare mutation

A

because DNA replication occurs with high fidelity

110
Q

Common mutation

A

because there is a lot of DNA being replated?

111
Q

Where can mutations take place?

A

Somatic cells or germ-line cells

112
Q

Are Somatic Mutations transmitted?

A

Not transmitted from one generation to another

113
Q

Are Germ-Line mutations transmitted?

A

May be transmitted to approximetly 50% of offspring

114
Q

What are the three categories that point mutations (base substitutions) can be based on?

A

1) silent (aka synonymous)
2) missense (aka nonsynonymous)
3) nonsense

115
Q

Silent mutation effect

A

no change in amino acid (aa) sequence. happens in reading frames because of redundancy in genetic code

116
Q

Missense mutation effect

A

mutation causes 1 aa to be substituted for another, changing the aa sequence

117
Q

Nonsense mutation effect

A

an amino acid codon is converted to a stop codon

118
Q

Classification of nucleotide insertion or deletions (indels) by their effect on aa sequence of protein?

A

1) indels cause frame shift that alter reading frame, creating wither nonsense or missense effects on protein except when indels occur in multiples of 3 nucleotides.
2) indels outside of reading frames usually have no effect on phenotype

119
Q

What are the three classifying mutations by effect on functional phenotype?

A

1) loss-of-function
2) gain-of-function (aka radical)
3) neutral

120
Q

What is loss-of-function mutation?

A

protein function completely of partly lost. Recessive inheritance

121
Q

What is gain-of-function (aka radical) mutation?

A

new gene product, or gene product in ‘wrong’ tissue. Dominant inheritance

122
Q
A
123
Q

What is neutral mutation?

A

missense mutations that result in non-significant change in protein function, because one chemically similar amino acid substituted for another, or occurs in a part of the protein that is not important for function

124
Q

Are transitions or transversion more common?

A

transitions

125
Q

Transition meaning

A

purine to purine, or pyrimidine to pyrimidine

126
Q

Transversion meaning

A

purine to pyrimidine, or pyrimidine to purine

127
Q

What is a forward mutation?

A

alters wild phenotype

128
Q

What is reverse mutation?

A

changes mutant phenotype back to wild phenotype

129
Q

What are suppressor mutations?

A

where the first mutation is suppressed by a second mutation

130
Q

What are the two types of suppressor mutations?

A

1) intragenic
2) intergenic

131
Q

What is a intragenic mutation?

A

suppressor mutation in the same gene

132
Q

What is a intergenic mutation?

A

suppressor mutation in a different gene

133
Q

How do mutations happen?

A

spontaneously or induced by physical and chemical agents

134
Q

What are the three types of spontaneous mutations?

A

1) tautomeric shifts (base tautomer’s) during DNA replication
2) DNA strand-slippage during DNA replication
3) Misalignment of homologous chromosomes during crossing over (recombination) at meiosis I.

135
Q

What do tautomer shifts allow?

A

For base-paring of rare form (C/A and T/G)

136
Q

Base tautomers cause incorrect base-paring during __

A

DNA replication

137
Q

What is DNA strand-slippage during DNA replication?

A

An insertion or deletion owing to slipped-strand mispairing during DNA replication

138
Q

What is a Mutagen?

A

agents that cause mutation

139
Q

Examples of mutagens

A

Radiation and Chemical mutagens

140
Q

Sources of radiation as a mutagen?

A

1) ionizing radiation: cosmic rays, x-rays, and gamma rays
2) ultraviolet radiation from sunlight

141
Q

How do chemical mutagens work?

A

1) base analogs
2) base modifying agents
3) intercalating agents

142
Q

What is the effect of ionizing radiation?

A

Create free radicals. Results in change stable molecules into a free radical or an ion, which can alter the structure of bases and break phosphodiester bonds in DNA

143
Q

What are the effects of Ultraviolet Radiation?

A

is an electromagnetic radiation of lower energy than ionizing radiation. Can still generate free radicals under some circumstances, but less likely to do so than higher energy radiation. Most common source: the sun

144
Q

What can cause thymine dimers?

A

ultraviolet radiation

145
Q

Pyrimidine dimers

A

TT or CC

146
Q

What do base dimers cause?

A

kink in structure, and can block DNA replication

147
Q

What corrects damaged DNA?

A

DNA repair enzymes

148
Q

How does nucleotide excision repair work?

A

1) protein recognizes mismatches
2) unwinds DNA in area of mismatch
3) excises out nucleotides
4) fills in correct nucleotides

149
Q

Xeroderma pigmentosum

A

an autosomal recessive genetic disorder of DNA repair, the ability to repair mutations cause by ultraviolet (UV) light is deficient

150
Q

What are base analogs?

A

Chemicals that appear similar to the normal bases in DNA, but cause incorrect base-paring and introduction point mutations during DNA replication.

151
Q

What is the 5-Bromouracil?

A

a nucleotide analog that resembles both thymine and cytosine

152
Q

What are the effects of 5-Bromuracil?

A

Like thymine, it will base pair with adenine, but when ionized it will base pair with guanine.

153
Q

When do mutagenic effect of 5-Bromouracil occur?

A

During DNA replication

154
Q

What are base modifying agents?

A

chemicals that modify groups on the normal bases in DNA that result in incorrect base-paring and introduce point mutations during DNA replication.

155
Q

What are intercalating agents?

A

chemicals that distort the normal stacking of bases in DNA resulting in insertion or deletion of a single base-pair during DNA replication. Planar (flat) molecules that insert between adjacent bases in DNA.

156
Q

How much do intercalating agents distort bases?

A

by 0.68 nm, the size of a base

157
Q

What does intercalating agents result in?

A

frame-shift due to insertion of a base

158
Q

T/F. Scientist have determine exactly which man-made chemicals are mutagenic.

A

False, there is uncertainty and disagreement about how many man-made chemicals are in use

159
Q

What is the ames test?

A

assay for chemical mutagenicity.

160
Q

What is an example of ames test use?

A

A simples method to measure the reversion of a mutant His- salmonella bacterial strain to His+ salmonella wild-type strain by potential mutagens.

161
Q

What can could make the chemical more or less mutagenic in ames test?

A

Live enzyme

BIOL 2030 (7 decks)

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