Exam 1 Flashcards
(129 cards)
1
Q
The entire set of genetic information in a given organism
A
Genome
2
Q
Where are circular chromosomes found
A
Cytoplasm in proks, mitochondria/chloroplasts in euks
3
Q
Where are linear chromosomes found
A
Nucleus
4
Q
How are circular chromosomes packaged
A
Loosely packaged in eukaryotes and prokaryotes
5
Q
How are linear chromosomes packaged
A
Compact around histone proteins
6
Q
Chromatin
A
Histone proteins and DNA (eukaryotes)
7
Q
Can we predict relative genome size based on the complexity of the organism
A
No; genome sizes can vary between groups
8
Q
Are the number of genes proportional to genome size
A
No
9
Q
What do all genes (proks and euks) contain
A
- Coding region (exons)
- Regulatory region
- Transcription termination
10
Q
Coding region
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Contains the information for the structure of the expressed protein
11
Q
Regulatory region
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Information on where and when a gene will be transcribed during development; usually upstream of the coding region
12
Q
Transcription termination
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the stop signal for where transcription should end; usually downstream of coding region
13
Q
Where did the radioactively labeled DNA end up after centrifugation in Hershey and Chase’s experiment
A
Pellet, at the bottom
14
Q
Monomorphic genes
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Genes with one common allele
15
Q
Polymorphic
A
Genes with several common alleles
16
Q
Wild-type allele for monomorphic genes
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The allele found on the large majority of chromosomes in the population
17
Q
Mutations
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Changes in DNA base sequences
18
Q
Forward mutation
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A mutation that changes a wild-type allele of a gene to a different allele; the resulting novel mutant allele can be either recessive or dominant to the original wild-type allele
19
Q
Reverse mutation/reversion
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Mutation that cause the mutant allele to revert back to wild type
20
Q
Substitution mutation
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Occurs when a base at a certain position in one strand of the DNA molecule is replaced by one of the other three bases; after DNA replication, a new base pair will appear in the daughter double helix
21
Q
Transitions
A
Type of substitution; one purine replaces the other purine or one pyrimidine replaces the other
22
Q
Transversions
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Type of substitution; one purine replaces pyrimidine or vice versa
23
Q
Point mutations
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Transitions, transversions, or SMALL deletions/insertions that effect ome of just a few base pairs and thus alter only one gene at a time
24
Q
True or false: although average mutation rates are low, there is large mutation variation rates across genes
A
True
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Do larger or smaller genes sustain more mutations
Larger; they are larger targets
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Are average mutation rates higher in multicellular eukaryotes or bacteria
Eukaryotes; many more opportunities exist for mutation to accumulate in the germ line
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Are there higher mutation rates in human sperm or human eggs
Human sperm
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What are the two kinds of events that initiation DNA changes (potential mutations)?
Either DNA can be damaged by chemical reaction or irradiation, or mistakes can happen when DNA is copied during replication
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What determines if a DNA change becomes a mutation
If repair of the damaged DNA occurs before next round of replication, then no mutation, if it doesn't get repaired before replication, the mutation becomes established permanently in both strands and heritable mutation is the outcome
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Depurination
Hydrolysis of a purine base from the DNA backbone; results in DNA replication introducing a random base opposite the apurinic site; causes mutation in the new strand 3/4 of the time
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Deamination
Removal of an amino group; can result in changing C to U; replication following deamination may alter a C:G base pair to T:A pair in future generations
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What does naturally occurring radiation do to DNA
They break the sugar-phosphate backbone
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3' to 5' exonuclease
A proofreading function of polymerase molecules; it recognizes a mispaired base and excises it
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Tautomers
Similar chemical forms that interconvert continually; usually each base is usually in the form in which they pair
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How can base tautomerization cause mutation
If the base in a template strand is in its rare tautomeric form when DNA polymerase arrives, the wrong base will be incorporated to the new chain because they pair differently
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Unstable trinucleotide repeats
3 base pair repeat unit within a gene, results in diseased alleles after replication
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Slipped mispairing
DNA polymerase often pauses as it replicates through repeat regions; one of the strands can slip relative to the other one; can result in trinucleotide repeat expansion
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How may somatic mutations in genes become carcinogens
They may be genes that help regulate the cell cycle
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Ames test
Used by the FDA to identify potential carcinogens; screens for chemicals that cause mutation in bacterial cells; asks whether a particular chemical can induce His revertants
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When is a compound a potential carcinogen according to Ames test
If His+ revertants are more common on the petri dish without histidine than a control plate with unexposed cells, the compound is a potential carcinogen
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How do toxicologists simulate the action of mammalian metabolism during the ames test
They add a solution of rat liver enzymes to the chemical under analysis; because the simulation isn't perfect, they ultimately assess inducing the agent in test animals diets
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Homology dependent repair
Uses the complement strand of damaged region of DNA to use as a template to resynthesize
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Base excision repair
- A type of homology dependent repair mechanism
- Enzymes called DNA glycosylases cleave an altered nitrogenous base the sugar of its nucleotide, releasing the base and creating an apurinic or apyrimidinic site
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What does cytosine change into when it is deaminated
Uracil
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Thymine dimers are caused by
UV light
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In an Ames test, what does the control sample contain
The suspected mutagen and salmonella bacteria that can synthesize histidine
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Process of base excision repair
- After glycoslyase has removed the base from its sugar leaving an AP site, the AP endonuclease makes a nice in the DNA backbone of the AP site, DNA exonucleases attack the nick and remoce nucleotides from the vicinity to create a gap in the damaged strand, DNA polymerase fills in the gap by copy other strand, ligase seals up backbone of repaired strand
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Nucleotide excision repair
Removes alterations that base excision cant repair because the cell lacks a DNA glycosylase that recognizes the problematic bases
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Process of nucleotide excision repair
UvrA and UvrB patrils DNA for irregularities, UvcB and UvrC cuts the damaged strand in two places that flank the damage, the gap is filled by polymerase and sealed with ligase
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How are double stranded break repaired
- Homologous recombination
- Nonhomologous end joining
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Homologous recombination
Uses complementary base pairing to repair breaks with non loss or gain of nucleotides
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Nonhomologous end joining
Can bring together DNA ends that were not previously adjacent to each other, a few base pairs can be added/lost
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Methyl-directed mismatch pair
Corrects polymerase errors; active only after replication
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Process of methly-directed mismatch repair
- Adenine methlyase puts methyl group on A of GATC sequence
- After replication, old template has mark, daughter strand that has wrong nucleotide, doesnt
- MutL and MutS detect and bind to the mismatched nucleotides
- They direct MutH to nick the new strand across the methylated GATC
- DNA exonucleases then remove all the nucleotides between the nick and just beyond the mismatch, leaving a gap on the new unmethylated stand
- Polymerase, ligase repairs strand
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How many chromosomes does the nuclei of a normal human cell carry
23 pairs; total of 46; each pair seems to be identical except for male sex chromosomes
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Mitosis
Nuclear division followed by cell division that results in two daughter cells containing the same number and type of chromosomes as the original parent cell
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Meiosis
Nuclear division that generates egg or sperm cells containing half the number of chromosomes found in other cells within the same organism
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Diploid
two matching sets of chromosomes
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What does the shorthand n in 2n stand for
The number of chromosomes in a gamete; a diploid cell would therefore be 2n
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Centromere
The specific location at which sister chromatids are attached to each other; each sister chromatid has its own centromere
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Constriction
When two sister chromatids are pulled together tightly, that they form a constriction where the two centromeres that they each individually have can't be resolved from each other
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Metacentric chromosomes
Centromere is more or less in the middle
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Acrocentric chromosome
Centromere is close to one end
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Homologous chromosomes
Chromosomes that match in size, shape, and banding; the two homologs of each pair contain the same set of genes, although they may carry different alleles
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Autosomes
Chromosomes not involved in sex determination; humans have 44 in matching pairs
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Sex chromosomes
In humans, the X and Y chromosomes, which determine the sex of an individual.
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Leptotene
First stage of prophase 1; The long thin chromosomes being to thicken
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Zygotene
Step 2 of prophase 1; Begins as each chromosome seeks out its homologous partner and the matching chromosomes become zipped together in a process called synapsis
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Synaptonemal complex
Protein structure that "zips" homologous chromosomes together in synapsis
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Pachytene
Step 3 of prophase 1; beings at the end of synapsis; crossing over occurs which results in the recombination of genetic material
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Crossing over
during meiosis, the breaking of one maternal and one paternal chromatid, resulting in the exchange of corresponding sections of DNA and the rejoining of the chromosomes. This process can result in the exchange of alleles between chromosomes.
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Diplotene
Step 4 of prophase 1: Gradual dissolution of the synaptonemal complex and slight separation of regions of the homologous chromosomes; the homologs of each bivalent remain merfed along chiasmata
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What do chiasmata represent
Sites where crossing over occured
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Diakinesis
Step 5 of prophase 1: Further condensation of chromatids occur (chromatids thicken and shorten); chiasmata remain
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Kinetochore in MEIOSIS
The kinetochore (that attaches to a microtubule emanating from spindle poles) of sister chromatids fuse so each chromosome only has one kinetochore
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Metaphase 1
Tetrads line up along metaphase plate; each chromosome of a homologous pair attaches to fibers from opposite poles via kinetochores
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Anaphase 1
Chiasmata dissolve; allows the maternal and paternal homologs to move toward opposite spindle poles
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Telophase 1
Homologs reach poles; Nuclear membrane begins to form around chromosomes at the poles
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What is meiosis 1 often called and why
Reductional division; the number of chromosomes is reduced to one half the normal diploid number
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Interkinesis
- Occurs between meiosis 1 and 2
- Similar to interphase but WITH NO DUPLICATION
- In some species chromosomes decondense, other don't
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Prophase 2
If chromosomes decondensed during preceding interphase, they recondense during prophase 2; at the end of prophase 2, the nuclear envelope breaks down, spindle apparatus re-forms
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Metaphase 2
The kinetochores of sister chromatids attach to microtubule fibers from opposite poles of the spindle apparatus
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Difference between metaphase 2 and mitotic metaphase
In metaphase 2, the number of chromosomes is one-half that in mitotic metaphase and in metaphase 2 the sister chromatids are no longer strictly identical because of crossing over in metaphase 1
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Anaphase 2
Connection between sister centromeres allow sister chromatids to move toward opposite spindle poles; similar to mitosis
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Telophase 2
Membranes form around the four daughter nuclei and cytokinesis places them in a separate cell
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Equational division
Used to describe meiosis 2; each daughter cell has the same number of chromosomes as the parental cell present at the beginning of the second division
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Nondisjunction
Failures in chromosome segregation during cell division, when either chromatids or homologs do not separate properly; they may travel together to the same pole and eventually become part of the same gamete
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Aneuploidies
Results from nondisjunction; condition in which individuals have extra or missing chromosomes
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What is down syndrome caused by
An extra copy of chromosome 21 (trisomy 21); example of aneuploidy
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Aspects of meiosis that contribute to genetic diversity in a population
- Independent assortment
- Crossing over
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Differences between meiosis and mitosis
- Mitosis occurs in all types of cells with membrane bound organelles; meiosis only occurs in germ cells within reproductive organs that produce haploid gametes
- Mitosis is a conservative mechanism (identical), meiosis is not since the cells are not identical to original cell or each other
- Mitosis produces 2 new daughter cells; meiosis produces four haploid cells
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Monosomic
Type of aneuploidy; individual lacking one chromsome; 2n-1
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Trisomic
Individual having a single additional chromosome; 2n+1
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When will meiosis result in the production of half trisomic and half monosomic aneuploids after fertilization with a normal gamete
When homologous chromosomes don't separate (nondisjunction) during meiosis 1
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When will meiosis result in the production of only two of the four resulting gametes being aneuploid after fertilization
If meiotic nondisjunction occurs during meiosis 2
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Missense mutation
Mutations that change a codon into a mutant codon that specifies a different amino acid
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Conservative substitution
mutations that substitute an amino acid in a protein with a different amino acid having similar chemical properties
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nonconservative substitutions
mutations that substitute an amino acid in a protein with a different amino acid with dissimilar chemical properties.
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Nonsense mutation
- A mutation in which a codon for an amino acid is changed to a stop codon, resulting in the formation of a truncated protein.
- Results in truncated proteins; lacks all amino acids between the mutant amino acid and the c-term of the normal polypeptide
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Ways in which mutations outside the coding sequence during transcription can alter gene expression
- Changes in the sequence of a promoter can make it difficult for RNA polymerase to associate with promoter; diminishes transcription
- Mutations in enhancers prevent transcription factor binding
- Mutations in a termination signal can diminish amount of mRNA produced
- Changes in splice acceptor/donor sites and branch sites that allow splicing to join exons can prevent splicing
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Ways in which mutations outside the coding sequence during translation can alter gene expression
- In proks, mutations affecting a ribosome binding site can lower the affinity of the mRNA for the small ribosomal subunit, decreasing translation efficiency and thus protein product
- Mutation in the 5' UTR that creates an AUG upstream of normal AUG could lead to premature translation
- A mutation in the 3' UTR that prevent poly-A polymerase binding would prevent translation
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Null/amorphic mutations
Abolish the function of a gene; for protein encoding genes, the mutation either prevents synthesis of the polypeptide or promote synthesis of a protein incapable of carrying out any function
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Are amorphic alleles usually dominant or recessive to wild-type alleles
Recessive; if the amount of protein produced by a wild-type allele is above the required threshold for the biochemical requirements of the cell, a heterozygote will be wild type
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Hypomorphic mutation
An allele that produces either less of a wild-type protein or a mutant protein with a weak but detectable function.
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Are hypomorphic alleles usually dominant or recessive to wildtype alleles
Recessive
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Haploinsufficiency
Rare situations in which one WT allele doesn't provide enough of a gene product to avoid a mutant phenotype; makes the loss-of-function mutant allele dominant to WT alleles
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Gain-of-functino alleles
Rare mutations that alter a gene’s function rather than disable it by enhancing the the function or conferring a new activity on the protein
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Are gain of function alleles usually dominant or recessive
Dominant; a single such allele by itself usually produces a protein that can alter phenotype even in the presence of a normal protein
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Why are dominant gain of function mutant alleles usually lethal when homozygous
They are pleiotropic
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Hypermorphic mutations
A mutant allele that generates either more protein than the wild-type allele or a more efficient protein.
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Neomorphic mutations
- A rare class of dominant gain of function allele
-Rare mutations that produce a novel phenotype due to production of a protein with a new function or due to ectopic expression of the protein.
- Huntingdon disease allele is an example
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Ectopic expression
Gene expression that occurs outside the cell type, tissue, or time where or when the gene is normally expressed.
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Dominant-negative/antimorphic
Block the activity of wild-type alleles of the same gene, causing a loss of function even in heterozygotes.
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Deletions
- A type of chromosomal rearrangment
- The loss of a block of one or more nucleotide pairs from a DNA molecule
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Duplications
- A chromosomal rearrangement where the number of copies of a particular chromosomal region is increased.
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Inversions
A 180-degree rotation of a segment of a chromosome relative to the remainder of the chromosome.
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Reciprocal translocations
A chromosomal rearrangement that results when two breaks, one in each of two nonhomologous chromosomes, yield DNA fragments that switch places and become attached to the other chromosome.
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How do chromosomal rearrangements come about
- Chromosomal breakage (produced by x-rays in some cases)
- Illegitimate recombination at sites of repeated DNA sequences
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How can a deletion occur
If a single chromosome suffers two double-stranded breaks and the broken ends are fused (through NHEJ for example) before the fragment rejoins
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Transposable elements
- DNA sequences whose copies move from place to place; a single genome may accumulate hundreds of thousands of copies of such an element
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Deletion heterozygote
- Del/+
- An individual who is surviving with a chromosome deleted for more than a few genes because the homolog has normal copies of the missing genes
- Can still have mutant phenotypes
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Gene dosage
The number of times a given gene is present in the cell nucleus.
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Reasons deletion heterozygotes can have a mutant phenotype
- Due to haploinsufficiency
- Vulnerability to mutation
- Uncovering recessive mutant alleles
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Tandem duplications
The repeated copies lie adjacent to each, either in the same order or reverse order
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Nontandem/dispersed duplications
The repeated copies are not adjacent to each other and may lie far apart on the same chromosome or on different chromosomes
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Why do duplications usually have no obvious phenotypic consequences
An additional dose of most genes does not affect normal cellular or tissue physiology
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What are reasons that duplication can sometimes have phenotypic consequences
- Certain traits may be particularly sensitive to an increase in the number of copes of a certain gene
- More rarely, a gene near one of the borders of a duplication has altered expression because it has a new chromosomal envrionment
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Unequal crossing over
Recombination resulting from such out of register pairing; generates gamemtes with increases to three and reciprocal decreases to one in the numbers of copies of the duplicated region
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