Final Exam Study!! Flashcards
(142 cards)
1
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Genomics
A
Study of genomes, or ALL the DNA of an organism
2
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Structural Genomics
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Architecture, genetic mapping, sequencing & assembly
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Comparative Genomics
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Multiple genomes allow for comparisons
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Functional Genomics
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What do all the genes do?
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Human Genome Project
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Initiated in 1990 and was completed 13 years later, but now genomes can be sequenced much faster!
6
Q
Every year a new vertebrate genome is sequenced, every week a microbial genome of ca. 2 million bp is sequenced-
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This rate is increasing! As of April 2020, 11,531 eukaryotes, 35,744 viruses, and 246,954 prokaryotes!
7
Q
The mapping or hierarchical approach
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Divide the genome into segments with genetic and physical maps, then home in on details
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The whole-genome or shotgun approach
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entire genome is broken into random, overlapping segments that are then sequenced
9
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Genetic Map
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Genetic crosses and frequency of crossing over are used with polymorphic genetic markers to map the location of genes on chromosomes.
Humans have 24 genetic maps - 22 autosomal (non sex chromosomes, and the X and Y chromosomes
10
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Sequence-tagged site
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Unique genetic markers in the genome, very helpful for genetic maps
11
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Physical Maps
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More detailed information about genetic markers obtained from genome sequence data
12
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Open Reading Frames (ORF’s)
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Computer searches for start codons and stop codons to identify areas that are potential genes
Only ORF’s with more than 100 codons are likely genes
13
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Genes with unknown functions
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Over 35% of genes in any organism (including humans) have no deducible function!
14
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The Human Genome
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Sequenced in 2003, Aprox. 21,000 protein-coding human genes, Aprox. 22,000 other human genes, Greatest amount of genetic variation is in Africa.
15
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Human Genome Variation
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80,000 years ago, there were only 10,000 humans on the planet! Human genomes vary by at least 9 million bp
16
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The genome of C. Elegans
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C. elegans is a hermaphroditic roundworm (1 mm) that lives in soils throughout the world- from egg to adult in 3 days.
The entire genome (6 chromosomes) was sequenced in 1998.
17
Q
Arabidopsis thaliana
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First flowering plant genome to be sequenced in 2000.
Model organism for genetics and development studies.
Analysis of genes found 25,500- more than humans!
100 genes are similar to disease-causing genes in humans, including breast cancer and cystic fibrosis
18
Q
Fugu
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Fugu is an unusual vertebrate because its genome size is only 400 Mb.
Very few introns, and few gene deserts, regions with little genes.
Many genes in Fugu and humans are similar, so finding a gene in Fugu makes it easier to find in humans.
19
Q
Bioinformatics
A
Is a marriage between biology with math and computer science. Can help to:
Find genes in a genome
Align sequences
Predict structure and function of genes
Figure out interactions between genes and gene products
Use genomes to figure out evolutionary relationships
20
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GenBank
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Database that contains millions of DNA sequences for every organism you can imagine
21
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Discontinuous or Discrete Traits
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Each trait has only a few distinct phenotypes
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Continuous Traits
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A wide distribution of phenotypes are possible
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Nature Vs Nurture
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Scientists have argued for decades about which is more important to phenotype: genetics or environment
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Multifactorial Traits
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Traits affected by a combination of genotype and environment
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Polygene Hypothesis
For quantitative traits says that multiple genes control the traits. Should make sense when environments impact is limited
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Quantitative Trait Loci
Chromosome regions with genes that affect quantitative traits
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How do we measure traits?
VP (phenotype) = VG (genotype) + VE (environment)
We can measure a subset of the population called a sample
Must be large enough to eliminate chance differences between sample and population
Must sample at random to avoid bias
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Mean (x), or average:
tells us the center of distribution of phenotypes = ∑xn/n
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Variance
how much individual observations spread out around the mean
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Standard Deviation
The square root of variance - provides the same information but in same units as measurements
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Pleiotropy
Where one gene affects multiple traits
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Correlation Coefficient
Measures the strength of association between two variables in the same experimental unit, usually individuals. To calculate correlation, we first need to calculate covariance.
The correlation coefficient ranges from –1 to 1
Absolute value (not considering sign) gives strength of correlation
1 is very strong- so increasing x always has an effect on y
0 is weak- increasing x has no effect on y
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Covariance
Amount of variation of two characters that is shared in an individual
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Regression
Tells us more precisely about the relationship of two variables, and predictions from data
Regression analysis can tell us how much of a trait is genetically determined
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Slope
Tells us how much of an increase in x corresponds to an increase in y
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ANOVA
Analysis of variance asks if two or more means or significantly different
If we reject the null hypothesis that differences are due to chance (usually p < 0.05), then we can say differences are due to differences in genetics or the environment
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Heritability
Proportion of a populations phenotype that is due to genetics and not environment
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Broad-sense heritability
Quantitative genetics are most interested to know how much VP is attributable to VG
H2B = VG/VP
Value can range from 0 to 1, with zero being no heritability and 1 being maximum heritability with minimal influence of environment
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Narrow-sense heritability
geneticists want to know how likely parents are likely to resemble offspring, which is most affected by additive variation
H2N = VA/VP
Narrow-sense heritability can track phenotypes from generation to generation, and helps predict changes from selection (artificial or natural)
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Limitation of Heritability Estimates
1. Broad-sense heritability does not define all of the genetic contributions to a trait: it only measures proportion of phenotype that is due to genetics, not the genes that affect the trait
2. Heritability does not indicate what proportion of a phenotype is genetic: heritability is based on variance of a population, not individuals
3. Heritability is not fixed for a trait: depends on genetic makeup and environment of a population, which can shift often
4. High levels of heritability for a trait does not imply that trait differences among populations is genetic: environment can have a major effect on phenotype even if heritability is high, so population differences may not be genetic
4. Traits shared by members of a family do not imply high heritability: similar family environments can lead to similar phenotypes regardless of genetics
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Calculations of heritability
Midparent value, or mean of mom/dad’s phenotype equals value for offspring if variation is due to additive genetic variation- gives a slope of 1
If slope is less than 1, gene interactions (epistasis) and environment are a factor
If slope is 0, environment is main factor
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Evolution
Genetic changes in a population over time
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Natural Selection
Individuals with certain traits leave more offspring than others
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Artificial Selection
Only selected individuals are bred, causing genetic changes over time
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friendly dogs & Williams syndrome
Hypersocial dog behavior is linked to mutations in GTF2I and GTF2IRD1 genes.
Deletions of these genes in humans leads to Williams Syndrome:
Affects 1 in 70,000 people
Elfin facial features
Cognitive difficulties
Tendency to love everyone
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Dog size controlled by one gene
Size controlled by IGF-1 gene: insulin-like growth factor, a hormone. Same gene and mutation responsible for human dwarfism
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Development
The irreversible process organisms undergo from single-celled zygote to multicellular organism.
Its an interaction of the genome, cell cytoplasm and environment, and involves a programmed sequence of events
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Totipotent cell
Has potential to be any cell in the body
| This is what the zygote begins as
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Determination
Process where genetics "programs" a cell to become specialized (fate) - often done through induction, or chemical signaling
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Differentiation
process in which determined cells undergo physical changes to become a specific cell type. e.g. Nerve cells, antibodies, etc.
controlled by gene expression- synthesis of specific proteins guides fate of the cell
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Morphogenesis
"generation of form", process or anatomical structure formation and cell shape and size changes
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Genetic programs regulate 3 Developmental processes:
DETERMINATION
- Individual cells are fated to become….
DIFFERENTIATION
- Individual cells change to actually become….
MORPHOGENESIS
- Structures form by changes in cell #, shape, position
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Model Organisms
Must have mutants that affect development, and involved genes must be mapped and cloned for study
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The development controversy
Experiments with carrots in 1950’s: differentiated cells could be used to grow an entire new carrot, so DNA is NOT lost during development
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Dolly - The first cloned sheep
Dolly the sheep was born after 277 eggs were used for SCNT (Somatic Cell Nuclear Transfer), which created 29 viable embryos. Only three survived until birth, and only one survived until adulthood.
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Lymphotcytes
White blood cells involved in immune response
Small lymphocytes include B and T cells
B cells develop in bone marrow when activated by an antigen (foreign protein on virus or bacteria), they from plamsa cells that make antibodies after a few days
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Clonal Selection
Cells with antibodies to an antigen are stimulated to proliferate and make more antibodies
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Immunoglobin's
Antibody proteins, with 2 identical short or light (L) chains, and 2 identical long or Heavy (H) chains.
The two arms of the Y-shaped antibody contain the antigen-binding sites, which attach to antigens and stimulate clonal selection
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Hinge Region
allows antibody arms to move independently, and bind to separate antigen sites to help disable infecting agents
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Somatic Recombination
Random DNA arrangments during B cell development that join different gene segments and exclude others
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testis-determining factor (TDF)
Genes on the Y chromosome code for TDF, which causes testis formation. The absence of the Y chromosome defaults to ovaries formation instead
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Cancer
a disease where eukaryotic cells are transformed - divide uncontrollably and abnormally.
Such cells can invade surrounding tissues, or metastasize (spread) through the lymphatic system or blood to other regions of the body
Cancerous cells can undergo oncogenesis and lead to tissue masses called tumors (aka, neoplasm)
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Tumors
Malignant - Can spread to other parts of the body
| Benign - Self contained and do not spread
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Cell Checkpoints
Regulatory molecules (cyclins and cyclin-dependent kinases) control these checkpoints
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Signal Transduction
Process of relaying a growth-stimulatory or growth-inhibitory signal after an extracellular factor binds to a cell
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Neoplastic Cells
(cancerous cell) divide uncontrollably because of mutations to genes for cell surface receptors, stimulatory factors, or inhibitory factors
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Familial Cancers
Some cancers seems to "run in the family", and thus have a hereditary component - however, most cancers are sporadic (not hereditary)
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Viruses
Some viruses introduce their genes into the host, disrupting cell cycle controls
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Cancerous Cells
Gives rise to cancerous cells, and this is what causes tumors
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Mutagens
Like X-rays, smoking and chemicals increase the rate of cancer. Thus mutations in genes affect risk of cancer
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Chromosomal mutations
can lead to cancer - chromosomal breakage affects gene expression, crucial for control of the cell cycle
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Oncogene
a gene that cause unregulated cell proliferation - transmitted by RNA tumor viruses (all are retroviruses) into genome of host
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Retroviruses
Duplicate their RNA genomes through DNA intermediate using reverse transcriptase.
An example is HIV- human immunodeficiency virus, which can cause AIDS-acquired immunodeficiency syndrome
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Transducing Retroviruses
Pick up cellular (DNA) genes (often oncogenes) into their RNA genomes, and transfer them to new host genomes
Most transducing retroviruses can not self replicate- they need “helper viruses” if the cell is infected with viruses that have replication genes
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Carcinoma
Epithelial origin (breast, colon, pancreas, and others)
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Sarcoma
a cancer of the connective or supportive tissue (bone, cartilage, fat, muscle, blood vessels) and soft tissue
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provirus genome
When retroviruses invade a cell, the RNA is released. and reverse transcriptase make a double-stranded DNA copy of the RNA genome called provirus genome
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Nonocogenic retroviruses
Direct their own life cycle but do not change the growth properties of the cells they infect
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DNA Tumor Viruses
They can cause cancer bur they do not carry oncogenes like RNA tumor viruses
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Proto-oncogenes
Normal genes similar to viral oncogenes
| When proto-oncogenes undergo mutation, they can become oncogenes that induce cancer in normal cells
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Growth Factors
Causes cell to grow and divide
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Protein Kinase
Enzymes that add phosphate groups to target proteins, thus altering their function
- protein kinases known to affect signaling pathways of cells, that are involved with growth factors
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Membrane-associated G proteins
Activated by growth factors to cell membrane receptors - involved in signaling cascade that activated transcription factors for specific genes
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Tumor Supressor Genes
in the 1960s, Henry Harris found that normal cells had tumor suppressor genes, that can suppress uncontrolled growth of cancerous cells
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apoptosis
Programmed cell death
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Retinoblastoma
Childhood cancer of the eye, before 4 years old. 90% treatable.
Hereditary form is worse- cancer appears earlier and usually involves BOTH eyes
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Alfred Knudson
1971: proposed a hypothesis (two-hit mutational model) to explain 2 forms of retinoblastoma
In the sporadic form, two mutations occur in eye cell - rare so it only happens in one eye
In hereditary form - one mutation is passed on by heredity - but 2nd mutation occurs in eye cell
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Mutator Gene
Any gene that increases the spontaneous mutation rates of other genes when it is in the mutant form
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Carcinogen
a natural or artificial agent (chemical, radiation), that increases a cell's risk of becoming cancerous
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Direct-acting carcinogens
Bind to DNA and mutate it
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Procarcinogens
must be converted by the body's metabolism to become carcinogenic
Both kinds of carcinogens induce point mutations- leading to cancer in some cases
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Cigarettes
contain @7,000 chemicals, including radioactive materials (polonium-210 & lead-210), cyanide, arsenic, and tar
If you smoke a pack or more of cigarettes a day = radiation exposure of > 300 chest x-rays/year
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Vaping
Smoking liquid forms of nicotine is NOT safe and highly addictive ( = cocaine, heroin)
Heavy metals from vaping devices (e.g., chromium) linked to brain damage and cancer
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Thymine Dimers
Caused by UV light, which disrupts A–T pairing, causes a bulge in DNA, disrupts DNA replication at bulge, and can lead to cell death (skin cancer)
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herpes simplex virus (HSV)
HSV-1 = usually oral herpes - 50-80% of adults in USA infected by age 20
HSV-2 = usually genital herpes - causes painful sores that last for several days or weeks- not correlated with cancer, but can increase chance of HIV
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Linked genes (syntenic)
Genes on the same chromosme
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Creighton, McClintock, and Stern
proved that Morgan’s idea of crossing over is correct
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Coupling
two wild-type alleles on one homolog, and two recessive alleles on the other
w+ m+ / w m
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Repulsion
has one wild-type allele and one mutant allele on each homolog
w+ m/ w m+
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Alfred Sturtevant
A student of Morgan's, Defined a map unit (mu) as the interval in which 1% of crossing over takes place- aka, centimorgan (cM)
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Crossover frequency
frequency of physical exchange between chromosomes in between genes of interest
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Recombination Frequency
Frequency of recombination of genetic markers (alleles) in a cross - determined by offspring phenotypes
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Centromere
Usually central constriction of chromosomes
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Metacentric
Centromere about centered
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Submetacentric
Centromere positioned so one arm is longer than the other
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Acrocentric
Centromere close to the end that P arm is so tiny, it is hard to observe (called a satellite)
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Telocentric
centromere is on the end, so chromosome has only one arm
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Holocentric
Entire chromosome acts as a centromere
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Sets of Chromosomes
Diploid organisms have two sets of homologous chromosomes, polyploids have more than two
Aneuploid - 'Unbalanced' chromosome number, often resulting in few offspring,
Euploid - 'balanced' chromosome number, normal fertility
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Obligate Parthenogenesis (OP)
females reproduce exclusively by asexual means - female produces eggs with two set of genes
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facultative parthenogenesis (FP)
Females that normally reproduce sexually turn to asexual reproduction, usually in the lack of males - females second polar body behaves like a sperm to activate and fertilize ovum for diploid zygote
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Nondisjunction
Failure of homologous chromosomes (Meiosis I) or sister chromatids (Meiosis II) to separate and move to opposite poles during Anaphase. Results in Aneuploidy - abnormal condition where one or more chromosomes of a normal set are missing or present in large numbers
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Nullisomy
One pair of homologous chromosomes is lost
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Monosomy
Loss of a single chromosome
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Trisomy
Gain of a single chromosome
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Tetrasomy
gain of an extra chromosome pair
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Trisomy-21
Common aneuploid chromosome disorder occurs in 1,430 per million live births- probability increases with age of mother- father’s age factors in too if mother is over 35
Leads to mental retardation, epicanthal folds over the eyes, short and broad hands, and below-average height
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Fragile X syndrome
after Down’s syndrome, leading cause of mental retardation in the United States- occurs in 1 in 1,250 males and 1 in 2,500 female because it is X-linked
Caused by repeats of FMR1 allele resulting in methylation of DNA and constriction site
Leads to narrowing of small areas at end of chromosome, which can break, leading to deletion of key genes
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Monoploidy
Individual has only one set of chromosomes instead of two (haploid)
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Polyploid
Have multiple sets of chromosomes beyond normal diploid set
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Type of polyploidy
Autopolyploid - originated by unreduced gametes of the same species during meiosis (small percentage)- can result in aneuploid gametes (example- potato)
Allopolyploid: originated by hybridization between closely related species (large percentage- very common in ferns)- all gametes are euploid
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Chromosome mutation
variations from the normal (wild-type) condition in chromosome structure or number
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Four major types of chromosome mutations:
1. Deletions- remove a section of DNA from the
chromosome
2. Insertions- add a section of DNA to the
chromosome
3. Inversions- flip a section of DNA around on the
chromosome
4. Translocations- move a section of DNA to a
different place in the genome, usually a different
chromosome
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Pseudodominance
where deletion of a dominant allele leads to unexpected expression of recessive phenotype because it is the only remaining copy of the gene
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Cri-du-chat Syndrome
Cri-du-chat syndrome is a heterozygous deletion of part of the short arm of chromosome 5
1 in 50,000 births results in this syndrome- children are mentally retarded, have a variety of physical abnormalities (including larynx to give weird cry), constant constipation, etc
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Duplications
A chromosomal mutation that results in the doubling of a segment of a chromosome.
1. Tandem- adjacent to each other
2. Reverse tandem- order of duplicated genes is
opposite to those of the original
3. Terminal tandem- duplicated segments arranged
in tandem at end of chromosome
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Inversion
When a loop forms in a chromosome, a small piece may undergo breakage and reunion, and invert the order of genes (180 degrees)
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Paracentric inversion
does not include the centromere
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Pericentric Inversion
Includes the centromere
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Translocation
a chromosomal mutation with a move of parts of a chromosome to a different place in the genome
Nonreciprocal intrachromosomal translocation: movement within same chromosome
Nonreciprocal interchromosomal translocation: movement from one chromosome to another in a one-way direction
Reciprocal interchromosomal translocation: two-way movement from one chromosome to another
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Reciprocal translocation
breakage and reunion of a piece of non-homologous chromosomes
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Fusion
two non-homologous acrocentric chromosomes undergo reciprocal translocation to form a metacentric chromosome. Form a “trivalent” with non-fused acrocentric chromosomes- can result in aneuploid gametes
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Fission
a metacentric chromosome breaks into two acrocentric chromosomes (rare)
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Position Effect
location of the gene (in a chromosome fragment) changes its expression when it moves to a different part of the genome
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pronucleus
haploid nuclei of eggs or sperm
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Genomic Imprinting
phenomenon where a gene’s expression depends on the parental origin of a gene copy
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Epigenetics
coined by Conrad Waddington in 1942, a heritable effect resulting from alteration of DNA (but not in the DNA sequence!) or chromatin during gametogenesis (epi = above)
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Gene Silencing
a gene is not expressed (i.e., turned off) because of a mechanism that is not from the DNA itself (not a mutation)
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Transcriptional gene silencing
transcription is blocked because the gene occurs in heterochromatin- transcriptional enzymes cannot get access to perfectly normal gene
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Post-transcriptional gene silencing
mRNA from a transcribed gene is destroyed or blocked, so no translation occurs
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RNAi pathway-
where microRNA (miRNA) or small interfering RNA (siRNA) blocks translation of targeted mRNA
Used as a defense against viruses, during development, and to regulate gene expression
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DNA methylation-
addition of methyl groups —CH3 to CG dinucleotides of imprinted DNA areas
DNA methylase recognizes methyl groups on one strand of the double helix and adds them to the opposite strand
