week 5 Flashcards
1
Q
Why can’t Mendelian inheritance fully explain genetic diversity?
A
only explains only a minority of phenotypes.
Phenotypes often depend on interactions among multiple genes.
2
Q
What is genetic determinism, and why is it flawed?
A
Genetic determinism is the oversimplified belief that genes alone determine traits or behaviors, ignoring the crucial roles of environmental factors and gene interactions.
3
Q
What is an example of gene-environment interaction in coat pigmentation?
A
The colourpoint locus in cats encodes an enzyme that produces pigmentation only at lower temperatures, resulting in darker fur on cooler body parts (ears, nose, feet, and tail) and lighter fur where the temperature is higher.
4
Q
What is genetic penetrance?
A
- proportion of individuals with a given genotype that shows an “expected” phenotype
- Same trait might show in some organisms and be absent in others (despite having the same allele for it)
5
Q
What penetrance is shown is 3 out of 5 has expressed the expected phenotype?
A
incomplete penetrance, phenotype is 60% penetrant
6
Q
What is expressivity?
A
is the degree of gene expression (could be influenced by environment )
7
Q
What is eugenics, and how is it linked to genetic determinism?
A
Eugenics is the flawed practice of limiting reproduction in certain groups to create a “fitter” population, based on the false assumption that human traits like poverty are solely determined by genetics.
7
Q
What defines complex traits, and how do they differ from Mendelian traits?
A
Complex traits are influenced by multiple genes and environmental factors, do not follow Mendelian inheritance, and vary based on the genetic architecture of specific populations.
8
Q
Complex traits: ___ genes with ___ and often ____ effects on phenotype
A
Complex traits: many genes with small and often additive effects on phenotype
9
Q
What is the difference between additive and non-additive gene action in complex traits?
A
Additive gene action occurs when alleles contribute fixed, cumulative effects to a trait, while non-additive variation, like dominance, means the trait value is not directly proportional to the number of alleles at a locus.
10
Q
What kind of distribution does continuous traits have?
A
Normal distribution
11
Q
What is broad-sense heritability (H²)?
A
Broad-sense heritability (H²) is the proportion of phenotypic variation in a population attributable to genetic factors, specific to the trait, population, and environment.
12
Q
phenotypic variation = ___ + ___
A
broad sense heritability + variation due to environment
13
Q
What is narrow-sense heritability (h²)?
A
the proportion of phenotypic variation due to additive genetic components
14
Q
How to calculate H2?
A
h2 + variation due to non-additive genetic components
15
Q
What does narrow-sense heritability (h²) indicate in breeding?
A
h² indicates which traits can be improved by artificial selection. Higher h² means more potential for selection to influence the trait.
16
Q
What happens if a trait has a heritability of 0?
A
If a trait has a heritability of 0, no control can be exercised over that trait, meaning artificial selection cannot affect it.
17
Q
What is the Selection Differential (S)? What is the Response Differential (R)?
A
Selection differential (S) is the difference between the means of the selected group and the base population.
Response differential (R) is the difference between the means of the offspring and the base population.
18
Q
How do you calculate heritability (h²)?
A
Heritability (h²) is calculated by dividing the Response Differential (R) by the Selection Differential (S):
h² = R/S
19
Q
What does h² indicate for evolution?
A
In evolution, h² indicates which traits can be affected by natural selection. Higher heritability means greater potential for evolutionary change.
20
Q
What are Quantitative Trait Loci (QTLs)?
A
QTLs are genomic regions that control the genetic variation of complex traits.
21
Q
How do QTLs contribute to phenotype?
A
QTLs have different alleles that make small, quantitative contributions to the phenotype of a complex trait.
22
Q
How is QTL mapping done?
A
QTL mapping involves crossing two lines that differ in the trait of interest and also differ at known marker loci. F1 individuals are crossed, and the phenotype is correlated with genetic makeup in the F2 generation.
23
Q
What is the purpose of marker loci in QTL mapping?
A
Marker loci help identify regions of the genome that are associated with the trait of interest by correlating marker segregation with the phenotype in the F2 generation.
24
What is the result of lack of recombination in QTL mapping?
The lack of recombination leads to a situation where markers associated with the QTL are inherited together with it, but the exact QTL location is broad and imprecise. Fine-tuning the mapping with additional markers and testing candidate genes helps narrow down the exact position of the QTL responsible for the trait.
25
What is a Genome-Wide Association Scan (GWAS) and how does it work?
GWAS identifies genetic variants linked to traits in natural populations, without controlled breeding crosses.
Assesses many alleles at once, using numerous markers to pinpoint narrow genomic regions associated with traits.
More recombination over time allows for fine-mapping of these regions.
26
What is linkage disequilibrium?
Degree to which one genetic variant is inherited (or correlated) with a nearby genetic variant in given population
27
What is pleiotropy and how does it relate to GWAS?
Pleiotropy occurs when a single genetic locus affects multiple distinct traits.
The same QTL may appear in multiple GWAS for different complex traits, with the same or different alleles involved.
27
What are the key SNPs in the APOE gene and how do they affect Alzheimer’s risk?
APOE Gene: Encodes apolipoprotein E, involved in lipid metabolism and cholesterol transport.
Key SNPs:
APOE ε2 (protective) – Reduced Alzheimer’s risk.
APOE ε3 (neutral) – Average Alzheimer’s risk.
APOE ε4 (risk) – Increased Alzheimer’s risk, especially with two copies of ε4.
28
What is the relationship between the 2 SNPs in each APOE variant?
They are in linkage disequilibrium - always inherited together regardless of closeness of loci.
29
What is the difference between clinical and direct-to-consumer (DTC) genetic testing?
Clinical Testing: Performed through healthcare providers; results reviewed and discussed with a doctor, who provides explanations and context.
Direct-to-Consumer Testing: Results given directly to individuals, often without healthcare provider involvement.
29
Lifecycle of a gene: organisms have variation in ___ and ____
genome size & genome composition
30
What is horizontal gene transfer
where genetic material are exchanged between different organisms that are not parent and offspring (between unrelated organisms)
30
Where do new genes come from?
1. Horizontal gene transfer (lateral gene transfer)
2. duplication of an existing gene
3. de novo (new) gene
31
How is horizontal gene transfer achieved?
can be through mechanisms: conjugation, transformation, transduction
32
What is Transformation in bacteria?
Transformation is the process where bacteria take up DNA from their environment.
33
What is Conjugation in bacteria?
Conjugation is the direct transfer of DNA between two bacteria.
It involves plasmids (circular DNA) and is transferred through a sex pilus.
34
What is Transduction in bacteria?
Transduction is when viruses or bacterial phages transfer DNA between bacteria.
The virus picks up DNA from a host bacterium, injects it into another, and incorporates it into the new bacterium's genome.
35
Give an example of the transfer of genes into nuclear genome of eukaryotes
e.g. endosymbiontic events (mitochondria & chloroplast) entering eukaryotes
36
Give an example of how genes were lost in organelles overtime
both mitochondria and plastids have about 5000 genes, over evolutionary time, genes were transfered into nuclear genome. organelles no longer needed to produce proteins themselves so they got rid of their genes.
37
What is Gene Duplication and its role in eukaryotes?
Gene duplication is the most common source of new genes in eukaryotes.
It can involve duplication of:
- Whole genome
- Whole chromosome
- DNA segments (including genes and exons)
38
What are the 2 ways to duplicate whole chromosomes?
- duplication by aneuploidy (autopolyploidisation)
- duplication by hybridisation (allopolyploidisation)
38
Briefly explain aneuploidy whole chromosome duplication
- meiotic error produces gametes with same number of chromosome as somatic cell
- followed by combination of gene into zygote which has twice the number of chromosome as parent
39
Briefly explain hybridisation whole chromosome duplication
- a and b are both diploid but with diff number of chromosomes
- hybridises with diploid combines w haploid gamete
40
What are the 3 ways of DNA segment duplication
- replication error
- unequal crossover
- retrotransposition
41
Explain how replication error leads DNA segment duplication
during DNA replication, a DNA loop may form which is stabilised by 2 additional sequences. in the next round of replication, if the strand with the loop is a template strand, repeat sequence occurs (expansion within repetitive region)
42
Explain how unequal crossover leads DNA segment duplication
during recombination, repetitive sequences can cause homologous chromosomes to line up improperly in chromosomes
43
Explain how retrotransposition leads DNA segment duplication
- transposable elements makes copies of themselves
- getting transcribed into rna and reverts transcribes themselves to DNA
44
What are De Novo (new) genes and how are they created?
De novo genes are created from non-coding DNA.
The sequence must acquire both an open reading frame (ORF) and be transcribed by RNA polymerase II to become a functional gene.
Many new genes are unique and not found in closely related organisms.
45
How are genes lost?
- Deletion
- Genetic drift
- Selection against
- Loss of function by mutation (pseudogenisation)
46
How are genes preserved?
- Compensation
- Neofunctionalisation
- Subfunctionalisation (temporal / specialisation)
- Lack of selection against / selection for
47
How are genes lost by deletion
- duplication occurs during DNA replication
- if DNA loop forms on template strand intead of nascent strand a deletion occurs
- called contraction in repetitive regions
48
How are genes lost by loss of function by mutation (pseudogenisation)
Loss of function occurs when mutations affect the function of a duplicated gene without being deleterious to the organism.
For example, a mutation in the start codon of a gene makes it non-functional, turning it into a pseudogene.
49
How are genes preserved by compensation?
Gene dosage compensation occurs when one copy of a gene is transcriptionally silenced (similar to X-inactivation in mammals), or transcription factors (TFs) are split between the gene copies.
The result is that the overall gene expression levels remain similar to before the duplication.
50
How are genes preserved by neofunctionalism?
Neofunctionalization occurs when a duplicated gene copy acquires an entirely new function.
51
Give an example of neofunctionaolism
Two fish families independently developed electric organs from duplicated Na+ channel genes. These organs allowed for new sensory modalities used in communication and hunting in complete darkness, and the original gene copies were lost
52
How are genes preserved by lack of selection against/selection for
Selection for more copies of a gene can occur under certain conditions.
53
Example of genes genes being preserved by lack of selection against/selection for
Humans with a high-starch diet have a higher average number of amylase gene copies, which encodes an enzyme for starch digestion.
Populations with high-starch diets, like some Japanese populations, can have up to 14 copies, while populations with low-starch diets have around 6 copies.
54
How are genes preserved by subfunctionalisation?
Subfunctionalization occurs when gene copies retain similar functions but specialize in a subset of functions or specific timing of use.
55
What are transposable elements?
pieces of DNA in our genome that is able to jump around
56
What is class 1 retrotransposon?
Retrotransposons are transcribed into RNA, then reverse-transcribed into DNA.
57
What is class 2 DNA transposon?
(machinery that cuts out the transposable element and gets inserted) - cut and paste
58
Which process can result in gene duplication?
Class 1 TE transposition only (RNA becomes DNA and gets inserted. donor is still there when new one has been copied = duplication)
58
How do transposable elements contribute to gene duplication in eukaryotes?
Transposable elements, when transcribed, can also transcribe the gene they are in front of.
Reverse transcriptase copies both the transposable element and the gene (RNA → DNA).
If the RNA is spliced before reverse transcription, the resulting copy of the gene (cDNA) lacks introns.
This creates a duplicated gene without introns, helping to discover new genes.
59
What most commonly happens to duplicated TEs
they are mutated and lose their ability to duplicate (pseudogenisation)
60
How do transposable elements (TEs) interact with telomeres in fruit flies?
In fruit flies, TEs (Class 1) copy themselves onto the ends of chromosomes, specifically the telomeres.
This insertion helps lengthen telomeres and protect against DNA shortening.
This creates a form of genic symbiosis where the genome and TEs cooperate for genome stability.
61
How will genomic evolution be affected by these TEs in fruit flied
Over generations, chromosomes will accumulate copies of TEs, unless there's strong selection against them or they undergo pseudogenisation.
Dosage compensation in mammals (like X-inactivation) balances gene expression between sex chromosomes.
In fruit flies, TEs inserted in telomeres do not require dosage compensation, as they integrate into heterochromatic regions where genes are not expressed.
62
What does "evolutionary developmental biology" (Evo-Devo) study?
how a phenotype arises through development (genetic and environmental processes) and why it persists in populations through evolutionary processes (natural selection).
63
What are the main components involved in the genetic basis of development?
Cis-acting elements: DNA regions like enhancers and promoters, which regulate gene expression.
Trans-acting elements: Transcription factors (TFs) that regulate gene expression distally.
64
What is the difference between cis-acting and trans-acting elements?
Cis-acting elements: Regulatory sequences near a gene (e.g., enhancers, promoters).
Trans-acting elements: Molecules like transcription factors that regulate gene expression from a distance.
65
How do transcription factors (TFs) regulate gene expression?
TFs bind to cis-acting elements (e.g., enhancers) to activate or repress gene transcription. Cooperative binding between TFs can enhance or stabilize gene expression.
66
How does cooperative binding create gene expression switches
proportion of cir element shows diff curve and threshold for expression is lower so conc of TF will be sufficient to trigger expression
67
What happens when a gene is bound by different transcription factors (TFs)?
When a gene is bound by different TFs, its transcription can be regulated in different cell types and at different times, depending on the combination of TFs and the inputs to its cis-acting regulatory regions.
68
How does signalling component affect development beyond transcription?
Developmental genes encode signaling pathways where ligands released by one cell bind to receptors on other cells, triggering a signal transduction cascade that activates transcription factors and changes gene expression.
69
How is the anterior-posterior axis established in Drosophila?
- Step by step process: expression of one set of genes governs expression of the next
- Genes encode TFs or signalling components
- Domain of expression gets progressively more restricted (shown by impact of mutations)
70
What is the role of the maternal effect gene Bicoid in Drosophila development?
Bicoid is a maternal effect gene whose mRNA is deposited in the egg by the mother. The translated protein forms an anterior-posterior (A-P) gradient in the embryo, with higher concentrations at the anterior end, influencing gene expression in a concentration-dependent manner.
71
How does the Bicoid protein influence gap genes like Hunchback in Drosophila?
Bicoid binds to the enhancers of gap genes (e.g., Hunchback), which are also transcription factors. This binding creates a concentration gradient, with different gap genes being activated in response to specific levels of Bicoid, establishing positional information along the anterior-posterior axis.
72
How do gap genes like Hunchback respond to Bicoid in terms of gene expression?
Gap genes contain cis elements with various arrangements of binding sites for Bicoid. Genes with low affinity for Bicoid are activated only at higher Bicoid concentrations near the anterior, while those with higher affinity are activated closer to the anterior-posterior boundary.
73
What is the function of pair-rule genes in Drosophila?
Pair-rule genes like Even-skipped are expressed in alternating stripes and refine the segmentation of the embryo, essential for body patterning.
74
What is the role of segment polarity genes in segmentation?
Segment polarity genes help establish the boundaries of segments and their polarity, ensuring proper segmental organization in the developing embryo.
74
What is the role of homeotic genes (Hox genes) in development?
Homeotic genes (Hox genes) determine the identity of repeated body units or segments in organisms. They do not control the formation of these segments (which is managed by earlier developmental genes), but rather specify what type of structure will form in each segment.
75
How are the 8 Hox genes organized, and what is their significance?
The 8 Hox genes are clustered in two complexes, each coding for transcription factors (TFs). The arrangement of these genes suggests a local duplication origin, with genes physically close together that share similar DNA domains.
76
What is cis element evolution?
Cis element evolution refers to changes in enhancer sequences that can lead to new traits.
77
How can a cis mutation result in the gain of a trait?
A mutation in the enhancer sequence can create a new transcription factor (TF) binding site, leading to higher gene expression and a resulting trait.
78
What is an example of cis mutation resulting in the gain of a trait?
In Drosophila, a mutation in the enhancer region of the yellow gene can create a new TF binding site. This leads to higher expression of the yellow gene, resulting in darker wing pigmentation. Other parts of the gene expression remain unaffected.
79
What does co-option mean in the context of gene evolution?
Co-option refers to the novel use of a pre-existing gene for a new function.
79
How do genetic pathways evolve via co-option?
For example, a subset of Hox genes that normally control anterior-posterior differentiation of the body are expressed in limbs to control proximal-distal differentiation.
80
Can a cis mutation result in the loss of a trait?
Yes, mutations in enhancer regions can also result in the loss of a trait. For example, a mutation in the pelvic enhancer in stickleback fish can prevent the expression of pelvic spines, which are otherwise used for defense against predators.
81
How does a cis mutation lead to the loss of pelvic spines in stickleback fish?
In stickleback fish, a mutation in the pelvic enhancer prevents transcription factor binding, leading to the loss of pelvic spine expression. The loss of this trait is due to different selective pressures in shallow water environments, where spines are not needed for defense against predators.
82
What is trans element evolution?
Trans element evolution involves changes in transcription factor (TF) expression or binding ability
83
How does trans element evolution occur?
Trans element evolution occurs when the addition or alteration of amino acid motifs within a TF allows it to interact with new proteins. This adds a new function while retaining the TF's original function.
84
What are developmental constraints?
Developmental constraints are limitations that reduce the evolvability of a trait
85
How do TFs binding to multiple genes create developmental constraints?
TFs that bind to multiple genes can cause pleiotropy, where a single genetic change affects multiple traits. This can limit the evolvability of a trait because a beneficial change in one trait might bring about negative consequences in another.
86
Describe what each of these genes are for:
1 - gap gene
2 - segment polarity gene
3 - pair rule gene
4 - Hox gene
5 - maternal effect gene
Gap Gene: define broad regions in the embryo along the anterior-posterior axis, establishing major body segments. They act early in development to divide the embryo into large, distinct regions.
Segment Polarity Gene:
set up the internal organization and polarity of each body segment. They ensure that each segment has a distinct anterior and posterior end.
Pair Rule Gene:
define the boundaries of alternating segments in the developing embryo. They create a pattern of stripes
Hox Gene:
determine the identity of body segments along the anterior-posterior axis. They specify what structures will develop in each segment, such as legs or antennae.
Maternal Effect Gene:
control early development by providing positional information. The mother deposits RNA and proteins into the egg that direct the embryo's initial development, such as defining the body axes.
87
What happens when there is a loss of function mutation in the Ultrabithorax (Ubx) gene?
Loss of function occurs if Ubx expression is abolished where it is normally active.
Ubx is a transcriptional repressor that prevents wing formation in the T3 segment of insects.
Recessive mutation in Ubx leads to loss of repression in T3, causing the formation of two sets of wings: one in the normal T2 segment and another in T3.
