Section 3 - Module 10 Flashcards
1
Q
What can influence eDNA?
A
temperature, pH, oxygen, light, microbes, salinity
2
Q
eDNA
A
environmental DNA
3
Q
What is the term for creating new genetic variation?
A
genetic engineering
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)
5
Q
What are the two general types of chromosomal variations?
A
1) chromosome rearrangement
2) variation in chromosome numbers
6
Q
What is chromosome rearrangement?
A
Changes in the STRUCTURE of individual chromosomes
7
Q
What is variation in chromosome numbers?
A
changes in the number of chromosomes. One or more individual chromosomes are added or deleted.
8
Q
What are the 4 types of chromosomal rearrangements:
A
1) deletion
2) duplication
3) inversion
4) translocation
9
Q
In deletions where can loss of a segment from a chromosome occur?
A
either internal or terminal
10
Q
how many breaks arises by terminal-ends breaking off?
A
one break
11
Q
How many breaks results from internal breaking and rejoining of incorrect ends?
A
two breaks
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)
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
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
15
Q
What does deletion along the span of a centromere result in?
A
acentric chromosome
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.
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
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.
19
Q
Why does chromosome variations matter?
A
genetic disorders
20
Q
What is Cri du chat cause by?
A
deletion of terminal segment on one chromosome in chromosome 5 pair
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
22
Q
What is simplest form of duplication?
A
tandem
23
Q
Why is duplication important for evolution?
A
extra copies of genes provide raw material for new genes and adaptations
24
Q
How can duplication cause problems (albeit rare)?
A
excess or unbalanced ‘dosage” of gene products (proteins) resulting from duplications
25
What percent of human genome consists of duplications?
5%
26
How does duplication occur? (the origins)
unequal crossing over of misaligned chromosomes during meiosis generates duplicates (and deletions)
27
How to detect duplications?
in alignment in prophase I of meiosis duplicated chromosome form a loop, also by various molecular methods that detect higher geen dosage
28
What are the evolutionary consequences of duplication?
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
29
What is a pseudogene?
a segment of DNA that structurally resembles a gene but is not capable of coding for a protein.
30
Consequences of neofunctionalization
source of new genes, creates multigene families (example: globin gene families)
31
How can gene dosage affect phenotype?
amount of protein synthesized is often proportional to the number of gene copies present, so extra genes can lead to excess proteins
32
Example of how gene dosage can affect phenotype?
Bar region in drosophila (X chromosome). More copies leads to fewer eye facets
33
What is chromosomal rearrangements inversion?
two breaks in a chromosome followed by reinsertion in the opposite orientation
34
What are the two types of inversions?
1) pericentric (different site of centromere)
2) paracentric (Same of of centromere)
35
Peri meaning
around
36
para meaning
beside
37
What are the effect if inversions on phenotypes? (although often there is non)
sometimes there is an affect on phenotype, driven by the change in position of the gene(s)
38
Consequences of inversion?
position effects (location matters-sometimes), change in position can later expression
39
Example of inversion consequences
Variegation in Drosophila. Genes in/near chromatin may not be expressed
40
Inversion consequences for recombination and production of gemetes?
suppression of recombination
41
Inversion consequences if no crossing over occurs?
gametes produced are usually because genetic information is not lost or gained
42
Inversion consequences if crossing over occurs?
outside of inverted regions = viable gametes. Withing inverted region = some nonviable games and reduced recombination frequency
43
What does crossing over look like for paracentric inversion?
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.
44
Dicentric chromatid
are chromosomes that have two centromeres.
45
What happens to dicentric chromatid?
is pulled apart during anaphase of meiosis I with such force that the chromosome breaks at random positions
46
What does crossing over withing the pericentric inversion look like?
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
47
What is chromosomal rearrangement translocation?
Exchange of segments between nonhomologous chromosomes, or to a different region on same chromosome. Can be reciprocal or non-reciprocal
48
Reciprocal meaning
two-way
49
non-reciprocal meaning
one-way
50
Short-term/immediate consequences of chromosome variations?
gene/chromosomes dosage effect including genetic disorders, positions effect, effects on recombination & fertility (including miscarriages)
51
Long-term/evolutionary consequences of chromosome variations?
pseudogenes, neofunctionalization, new adaptations
52
What are the consequences of reciprocal translocation?
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)
53
Example of reciprocal translocation consequences?
'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)
54
What do inversion suppress?
recombination
55
How do inversion suppress renominations?
lack of recombination within inversion means that genes within the inversion are free to diverge to produce different adaptations
56
Example of inversion suppressing recombinations?
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!!
57
What are the tree types of European wading sandpiper?
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
58
What European wading sandpiper has cross 2 inverted?
not viable
59
What European sandpiper has cross two not inverted?
'independent' male
60
What European sandpiper has cross of inverted and not inverted?
faeder male
61
T/F. Genes within alternate orientations of inversion can diverge dramatically even though there is no divergence anywhere else in the genome.
True
62
Effect of inside inversion (European sandpiper)
large divergence
63
Effect of outside inversion (European sandpiper)
zero divergence
64
Is there recombination within inversion?
No
65
Chromosomal rearrangements of temperate adaptions and migratory behavior in Atlantic cod?
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
Aneuploidy
increase or decrease int he number of individual chromosomes, e.g. trisomy
67
trisomy meaning
three copies of a chromosome
68
polyploidy
increase in the number of sets of chromosomes, e.g. triploid
69
triploidy meaning
three copies of every chromsome
70
'Ploidy'
refers to the total number of chromosomes
71
'somy'
refers to the number of particular chromosomes
72
Nullisomy
loss of both members of a pair of homologous chromosomes (2n -2 = 44)
73
Monosomy
loss of a single chromosome (2n - 2 = 45)
74
Trisomy
gain of a single chromosome (2n +1 = 47)
75
Tetrasomy
gain of two homologous chromosomes (2n + 2 = 48)
76
What is nondisjunction?
failure of homologous chromosomes or sister chromatids to separate
77
Origins of aneuploidy
1) nondisjunction in meiosis or mitosis
2) deletion of a centromere leads to chromosome loss
78
Are trisomy viable?
may be viable
79
are monosomy viable?
usually not viable, except for sec chromosomes
80
Effect of trisomy 13
patau syndrome (1/16000)
81
Effect of trisomy 18
Edwards syndrome (1/5000)
82
effect of trisomy 21
down syndrome (1/800)
83
effect of monosomy X (XO)
turner syndrome (girls)
84
Effect of extra copies of the X chromosome (e.g. XXY - most common, XXXY)
Klinefelter syndrome (males)
85
What is the most common abnormality
trisomy
86
What is trisomy thought to be the most common cause of?
spontaneous abortions or miscarriages
87
In most cases of down syndrome who is contributing to the extra chromosome?
The mother approximately 75% of the time
88
What causes most cases of familiar down syndrome?
Arise in offspring's of parent who carry a chromosome that underwent Robertsonian translocation
89
Robertsonian translocation
exchange of long arms of non-homologous acrocentric chromosomes
90
What is one of the smallest chromosomes?
Chromosome 21
91
What does it mean for a gene to be present as a mosaic?
not all cell have it
92
Do plants or animals tolerate aneuploidy better?
plants
93
Why do plants tolerate aneuploidy better?
usually viable; phenotypes maybe altered and fertility reduced
94
Is it more common for plants or animals to be polyploidy?
plants
95
Effect of polyploidy on mammals and birds?
not known, but presumably lethal
96
What percent of angiosperms evolved via some form of polyploidy?
30-35%
97
What are the two types of polyploidy?
1) autopolyploid
2) allopolyploid
98
Autoploid
multiples of the same genome
99
Allopolyploid
multiples of closely related genomes
100
When can the origins of autopolyploid occur?
mitosis or meiosis
101
Nondisjunction of ______ during mitosis in early embryo can produce autotetraploid?
ALL chromosomes
102
Diploid gamete + normal gamete =
autotriploid (3n)
103
Diploid gamete + diploid gamete =
autotetraploid (4n)
104
Effects of autopolyploidy
usually sterile (odd-numbered ploidy), most gametes produced are genetically unbalanced
105
What is required to convert sterile hybrid into fertile 'new' species?
chromosome doubling (hybrid is sterile, unbalanced gametes are nonviable), BUT if entire genomes doubled by mitotic nondisjunction, the fertility problem is fixed
106
Significance of polyploid in agriculture
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
Issues with polyploidy (bananas example)
"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
A mutation can either be __
rare or common (but ultimate source of all genetic variation)
109
Rare mutation
because DNA replication occurs with high fidelity
110
Common mutation
because there is a lot of DNA being replated?
111
Where can mutations take place?
Somatic cells or germ-line cells
112
Are Somatic Mutations transmitted?
Not transmitted from one generation to another
113
Are Germ-Line mutations transmitted?
May be transmitted to approximetly 50% of offspring
114
What are the three categories that point mutations (base substitutions) can be based on?
1) silent (aka synonymous)
2) missense (aka nonsynonymous)
3) nonsense
115
Silent mutation effect
no change in amino acid (aa) sequence. happens in reading frames because of redundancy in genetic code
116
Missense mutation effect
mutation causes 1 aa to be substituted for another, changing the aa sequence
117
Nonsense mutation effect
an amino acid codon is converted to a stop codon
118
Classification of nucleotide insertion or deletions (indels) by their effect on aa sequence of protein?
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
What are the three classifying mutations by effect on functional phenotype?
1) loss-of-function
2) gain-of-function (aka radical)
3) neutral
120
What is loss-of-function mutation?
protein function completely of partly lost. Recessive inheritance
121
What is gain-of-function (aka radical) mutation?
new gene product, or gene product in 'wrong' tissue. Dominant inheritance
122
123
What is neutral mutation?
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
Are transitions or transversion more common?
transitions
125
Transition meaning
purine to purine, or pyrimidine to pyrimidine
126
Transversion meaning
purine to pyrimidine, or pyrimidine to purine
127
What is a forward mutation?
alters wild phenotype
128
What is reverse mutation?
changes mutant phenotype back to wild phenotype
129
What are suppressor mutations?
where the first mutation is suppressed by a second mutation
130
What are the two types of suppressor mutations?
1) intragenic
2) intergenic
131
What is a intragenic mutation?
suppressor mutation in the same gene
132
What is a intergenic mutation?
suppressor mutation in a different gene
133
How do mutations happen?
spontaneously or induced by physical and chemical agents
134
What are the three types of spontaneous mutations?
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
What do tautomer shifts allow?
For base-paring of rare form (C/A and T/G)
136
Base tautomers cause incorrect base-paring during __
DNA replication
137
What is DNA strand-slippage during DNA replication?
An insertion or deletion owing to slipped-strand mispairing during DNA replication
138
What is a Mutagen?
agents that cause mutation
139
Examples of mutagens
Radiation and Chemical mutagens
140
Sources of radiation as a mutagen?
1) ionizing radiation: cosmic rays, x-rays, and gamma rays
2) ultraviolet radiation from sunlight
141
How do chemical mutagens work?
1) base analogs
2) base modifying agents
3) intercalating agents
142
What is the effect of ionizing radiation?
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
What are the effects of Ultraviolet Radiation?
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
What can cause thymine dimers?
ultraviolet radiation
145
Pyrimidine dimers
TT or CC
146
What do base dimers cause?
kink in structure, and can block DNA replication
147
What corrects damaged DNA?
DNA repair enzymes
148
How does nucleotide excision repair work?
1) protein recognizes mismatches
2) unwinds DNA in area of mismatch
3) excises out nucleotides
4) fills in correct nucleotides
149
Xeroderma pigmentosum
an autosomal recessive genetic disorder of DNA repair, the ability to repair mutations cause by ultraviolet (UV) light is deficient
150
What are base analogs?
Chemicals that appear similar to the normal bases in DNA, but cause incorrect base-paring and introduction point mutations during DNA replication.
151
What is the 5-Bromouracil?
a nucleotide analog that resembles both thymine and cytosine
152
What are the effects of 5-Bromuracil?
Like thymine, it will base pair with adenine, but when ionized it will base pair with guanine.
153
When do mutagenic effect of 5-Bromouracil occur?
During DNA replication
154
What are base modifying agents?
chemicals that modify groups on the normal bases in DNA that result in incorrect base-paring and introduce point mutations during DNA replication.
155
What are intercalating agents?
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
How much do intercalating agents distort bases?
by 0.68 nm, the size of a base
157
What does intercalating agents result in?
frame-shift due to insertion of a base
158
T/F. Scientist have determine exactly which man-made chemicals are mutagenic.
False, there is uncertainty and disagreement about how many man-made chemicals are in use
159
What is the ames test?
assay for chemical mutagenicity.
160
What is an example of ames test use?
A simples method to measure the reversion of a mutant His- salmonella bacterial strain to His+ salmonella wild-type strain by potential mutagens.
161
What can could make the chemical more or less mutagenic in ames test?
Live enzyme
