Fundamentals! Flashcards

(184 cards)

1
Q

what are mendels three laws? define each

A
  1. law of dominance
  2. law of segregation
  3. law of independent assortment
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2
Q

What is Mendel’s law of dominance?

A

if a dominant allele is present in the genotype it will be expressed in the phenotype

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3
Q

What is Mendel’s law of segregation?

A

there are two copies of each gene (maternal and paternal) which are separated in meiosis, so each gamete has one copy of each gene and only one allele

Basically: gemetes’ ploidy number = 1

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4
Q

What is Mendel’s law of independent assortment?

A

alleles for separate traits are inherited independently of each other

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5
Q

What is the expected ration you would achieve for the F2 of a cross for a phenotypic trait with one dominant and one recessive parent in (P0)?

A

3:1
- 3 of the dominant phenotype
- 1 of the recessive phenotype

F1 would be the dominant phenotype (heterozygous)

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6
Q

how can you check that the outcome of a cross is following the mendelian phenotypic ratios?

A

use a chi squared stat test to compare the expected ratio eg 3:1 or 9:3:3:1 with the observed ratio

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7
Q

What significance level do you compare the chi squared value obtained to?

A

5% or 0.05

These are the same thing just expressed as a decimal and a percentage

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8
Q

What is the null hypothesis when performing chi squared tests?

A

That the phenotypic ratio is as expected - therefore if the chi squared value is below the critical value at 5% significance, this is accepted

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9
Q

Define Autosomal

A

When a trait is inherited independently of sex

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10
Q

What does monogenic mean?

A

The trait is controlled by a single gene (rather than multiple)

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11
Q

What is the ploidy number of gametes (sex cells that undergo meiosis)?

A

1n

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12
Q

What stage of meiosis introduces genetic variance?

A

Prophase I

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13
Q

What is the proper word for ‘crossing over’ over genetic info as seen in prophase 1?

A

Recombination

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14
Q

What is a test cross used to find? What is done?

A
  • It is used to determine the genotype of a dominant phenotype (whether it is homozygous or heterozygous dominant)
  • You cross the individual in question with a homozygous recessive individual
  • If all offspring is dominant, the parent genotype is likely homozygous dominant
  • If offspring is mixed, then the parent genotype is heterozygous
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15
Q

what is a reciprocal cross and why would you do one?

A

doing two crosses with the same traits being observed but swapping the sex of the parents to see if the trait is sex linked. eg cross a white eyed male fly with a wild type female and then cross a white eyed female fly with a wild type male. if each cross gives the same result it is an autosomal trait, if they give different results its a sex linked trait

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16
Q

describe crossing over/homologous recombination. what does this form? why does it occur?

A

crossing over occurs in prophase 1 when two homologous non-sister chromatids fuse at a chiasma and then break at this point, exchanging alleles in the process and producing recombinants. this increases genetic variation.

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17
Q

what are monohybrid and dihybrid crosses? what are the resulting genotypic ratios if the parents are heterozygous for both traits?

A

a monohybrid cross is used to examine one trait (ratio 3:1 )but a dihybrid cross examines two unlinked traits (ratio 9:3:3:1).

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18
Q

what can be inferred about two genes if a 9:3:3:1 ratio isn’t produced from a dihybrid cross where the parents are heterozygous for both traits.

A

the genes must be linked and this means they are on the same chromosome and are most likely to be found close together

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19
Q

list the four types of large, chromosomal mutations that can occur

A
  1. Duplication
  2. Deletion
  3. Inversion
  4. Translocation
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20
Q

give three ways that a large chromosomal deletion can occur and give a description of each

A
  1. Transposons: ‘jumping DNA’ some transposition events cause a region of the genome to be deleted when the transposon moves
  2. Incorrect DNA repair: sometimes 2 broken pieces of DNA are joined together missing another bit of the sequence inbetween
  3. Non-disjunction: chromosomes may not seperate properly during meiosis and so the individual has monosomy (one less chromosome than there should be)
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21
Q

What is the name of the condition we need to know where a deletion of part of a chromosome occurs?

A

Cri du chat syndrome

Means cry of the cat in French

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22
Q

describe the banding system of chromosomes

A
  1. chromosome number
  2. arm (p arm - small arm (petite) q arm- long arm)
  3. region
  4. band
  5. sub-band

regions, bands and sub-bands are numbered from the centromere outwards

p for petite!

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23
Q

what is the significance of duplications when both copies are retained?

A
  • They can lead to new phenotypes - opportunity for phenotypic novelty which may provide an evolutionary advantage
  • One copy of the gene may evolve a new function leading to diversification of species
  • Both copies may alternatively share the original function between them
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24
Q

what are copy number variations (CNVs)

A

short repeated dna sequences throughout the genome with variable number of repeats in each individual eg. tandem repeats

5-10% of the genome

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25
what are the three types of tandem repeats?
- Tandem repeats: a DNA sequence is duplicated and the new sequence is found next to the original sequence - Reverse tandem repeats: where the duplicated sequence is found next to the original sequence but has been inverted - Terminal tandem repeats: when a sequence found at the end of a chromosome is duplicated.
26
What is the condition caused by a duplication mutation that we need to know?
Trisomy-21 (Down syndrome) - extra copy of chromosome 21
27
What is Turner syndrome?
missing X chromosome in females
28
What is the difference between a conservative and non-conservative mutation?
- Conservative = the function of the gene has been retained despite the mutation - Non-conservative = the function of the gene has not been retained
29
What is the condition caused by translocation that we need to be aware of?
The Philadelphia chromosome - Reciprocal Translocation between chromosomes 9 and 22 - Causes cancer ## Footnote due to a gene fusion between abl and bcl which leads to protein fusion
30
What is a silent mutation?
Where a single nucleotide changes, but the amino acid produced in the protein chain still remains the same ## Footnote Protein made is therefore the same too
31
What is the difference between a pericentric inversion and a paracentric inversion
A pericentric inversion doesn't include the centromere and a paracentric inversion does.
32
What is a nonsense mutation?
- Where the nucleotide sequence is changed, instead producing a stop codon - This results in a truncated protein - The allele may lose its function if this occurs
33
Why do inversions and translocations impact meiosis?
they move the position of genes within the chromosome so that when the chromosomes pair up for homologous recombination the homologous genes are not aligned properly
34
name the three types of translocation
- intrachromosomal (within a c'some) - interchromosomal(between c'somes) - reciprocal (when genetic informatio is exchanged - can only happen with interchromosomal)
35
what can translocations lead to?
leads to gene fusions which can also result in protein fusions which can impact protein function or give it a new function. ## Footnote e.g. Philadelphia chromosome causes cancer
36
what does it mean that the genetic code is redundant/degenerate?
only the first two bases determine the amino acid and the third base can be variable. **There is more than one codon for the same amino acid**.
37
What is haploinsufficiency
When there is only one copy of a gene due to a deletion for example, and there is not enough protein being produced as a result. ## Footnote Basically: where one copy of a gene is not enough to produce a functional protein
38
What is disjunction?
The normal separation or moving apart of chromosomes toward opposite poles of the cell during cell division | Like an Irish guy saying 'this junction' so they split at the junction ## Footnote Non-disjunction is the opposite where this does not occur correctly
39
What are indels?
Changes in DNA sequences where one or more nucleotide bases are added/removed (insertion/deletion)
40
How did Morgan's experiments confirm the chromosomal theory of inheritance?
- Found a male white-eyed fly - Crossed with wild type female - Discovered sex linkage
41
What is linkage?
The tendency of genes that are closer together on a chromosome to be inherited together
42
What does variation in recombination frequency tell you?
It indicates the actual distances separating the genes on the chromosomes ## Footnote The further the distance between the linked genes, the greater the chance of crossover and therefore recombination
43
What is the equation for the recombination frequency?
RF = number of recombinant progeny / total number of progeny x 100
44
How can you tell whether a gene is on a sex chromosome or an autosome?
- If mostly males are affected, it is sex-linked - If equal affliction, it is likely autosomal
45
What is a polygenic trait?
A trait controlled by multiple genes
46
What is incomplete dominance?
Both alleles are expressed in the phenotype, usually leading to an intermediate or different phenotype ## Footnote Different to co-dominance, don't get them confused!!
47
What causes oculocutaneous albinism?
Mutations in tyrosinase to the OCA gene - causes melanin to be expressed abnormally
48
What is co-dominance?
Neither allele is dominant or recessive - both are equally expressed in the phenotype
49
What is the difference between co-dominance and incomplete dominance?
- Co-dominance = expressed alongside eachother - think of it like a patchwork pattern (e.g. A + B blood = AB child) - Incomplete dominance = expressed as a blend of eachother - think of it like mixing paint colours (e.g. white + red snapdragon = pink offsping)
50
What is an epistatic gene? Give an example of an epistatic gene
- An epistatic gene is a gene that modulates the expression of anothe gene - regardless of dominance - Example: coat colour in labradors ## Footnote Think 'epi' as in epigenetics means to change
51
What is haplosufficiency?
One functional copy of the gene is enough to make a normal phenotype
52
What is an allelic series?
A range set of difference alleles from the same gene
53
What is sex linkage?
- The shorter male Y chromosome has less genetic info - It therefore has fewer copies of certain genes - If they recieve a mutated copy of one gene, they must express this phenotypically if the Y chromosome does not posess a second copy
54
What kind of inheritance applies to mitochondrial/chloroplast genes?
Non-Mendelian ## Footnote This is because organelle transmission doesn't follow Mendelian laws
55
Ras is a very infamous oncogene. What is the common gain of function mutation occurring in Ras?
G12D missense mutation | Glycine at posititon 12 --> aspartate (D)
56
What are most gain of function alleles?
Dominant - their phenotype is displayed
57
What are most loss of function alleles?
Recessive - a single copy of the gene doesn't cause a phenotype | You can therefore have carriers of this type of mutation
58
What is the heterozygote advantage?
The fitness of the heterozygote is higher than the fitness of the homozygote - e.g. malaria and sickle cell disease CARRIERS ## Footnote Carriers dont have the disease, and are less likely to contract malaria. Homozygotes are less fit for survival whether they are wild type or whether they have sickle cell
59
What is pleiotropy
Where one gene can have multiple effects of an organism's phenotype ## Footnote e.g. sickle cell disease allele causes: the disease, provides malaria resistance, production of abnormal beta-globin, reduced RBC at high altitiudes
60
What is an amorph?
A mutant allele that has completely lost its function that produces a non-functional protein or no protein at all ## Footnote e.g. to have cystic fibrosis you must have 2 amorphic copies of the gene
61
What is a hypomorph?
A mutant allele that results in a partially functional protein | less effective than wild type, more effective than an amorphic allele
62
What is the difference between a transition and a transversion?
- Transition: substitute one purine for another, or one pyrimidine for another - Transversions: substitute a purine for a pyrimidine or vice versa
63
Which are the purines and which are the pyrimidines?
- Purines: A and G - Pyrimidines: C and T ## Footnote Purines are the big ones, pyrimidines are the smaller ones
64
Why is the substituation of a purine for an pyrimidine an issue?
A purine + pyrimidine is the perfect size. 2x pyrimidines would be too small, and 2x purines would be too big for DNA
65
What is the penetrance of an allele?
The percentage of individuals with a given allele who exhibit the phenotype associated with that allele
66
What can alter the penetrance of an allele?
- Interacting genes in the rest of the genome - e.g. modifiers, epistatoc genes, suppressors - Influence of the environemnt - e.g. how twins look more different based on the environment they grown up in ## Footnote Also whether the individual dies before it can be expressed (e.g. in Huntington's)
67
What is expressivity?
The degree to which an allele is expressed at the phenotypic level | Measures the intensity of the phenotype ## Footnote Interacting genes and the environment both influence the expression of the phenotype
68
Define allele
A variant form of a gene found at a specific locus on a chromosome.
69
Define autosome
A chromosome that is not a sex chromosome; humans have 22 pairs.
70
Define back cross
A cross between a hybrid organism and one of its parents or a genetically similar organism.
71
Define bivalent
A pair of homologous chromosomes aligned during meiosis I.
72
Define centromere
The region of a chromosome where the sister chromatids are joined and where spindle fibers attach during mitosis and meiosis.
73
Define chromatid
One of two identical halves of a duplicated chromosome.
74
Define chromosome
A structure of DNA and protein that carries genetic information in the form of genes.
75
Define codominance
A form of inheritance where both alleles are equally expressed in the phenotype.
76
Define complementation
Complementation occurs when two individuals with different homozygous recessive mutations (but with the same phenotype, like being unable to synthesize an enzyme) are crossed, and their offspring have a normal (wild-type) phenotype.
77
Define diploid
A cell with two complete sets of chromosomes (2n), one from each parent.
78
Define dominant
An allele that is expressed in the phenotype even when only one copy is present.
79
Define epistasis
A genetic interaction where one gene masks or modifies the expression of another.
80
Define F1 generation
The first filial generation; offspring from a cross of two parental organisms.
81
Define F2 generation
The second filial generation; offspring from a cross between two F1 individuals.
82
Define gamete
A reproductive cell (sperm or egg) with a haploid set of chromosomes.
83
Define gene
A sequence of DNA that codes for a functional product, typically a protein.
84
Define genetic interaction
The phenomenon where different genes influence each other’s expression.
85
Define genotype
The genetic makeup of an organism in terms of its alleles.
86
Define haploid
A cell with only one complete set of chromosomes (n).
87
What is independent assortment frequency directly proportional to?
Distance between genes on a chromosome - the further/more weakly linked the genes are, the more likely it is independent assortment will take place
88
What kind of nucleotide mutations makes a stop codon?
Nonsense
89
What are the 2 mechanisms of transposon movement?
Cut and paste Copy and paste
90
What are the 2 different categories of nucleotide mutations?
Point Frame shift
91
What causes chronic myelogenous leukemia?
A translocation A reciprocal translocation between human chromosomes 9 and 22 * Results in fusion of two different genes (abl and bcl). * This makes a protein fusion between the two products
92
Why is monosomy (too few gene products) worse than trisomy (too many)?
In monosomy, you're missing one entire set of alleles → potential loss of essential gene functions → haploinsufficiency and unmasked recessive mutations. In trisomy, all genes are present, just overexpressed
93
Give an example of a simple Mendelian trait
Red hair
94
What kind of trait is Oculocutaneous albinism?
Autosomal recessive
95
What deficiency is classic OCA caused by?
Tyrosinase deficiency, involved in melanin biosynthesis, therefore this leads to hypopigmentations
96
What kind of inheritance are most kinds of ocular albinism?
X-linked
97
What is an example of codominance?
Bell pepper colour - at least 3 loci involved AB human blood type
98
What is an example of incomplete dominance?
Pink snapdragon from red and white snapdragons
99
How does the O blood type happen?
No A or B gene - instead has 2 ii genes
100
What does a pedigree analysis show?
A pedigree shows the inheritance of traits across generations Squares = males, Circles = females, shaded = affected.
101
What is an epistatic gene?
Epistasis occurs when the effect of one gene is dependent on the presence of one or more 'modifier genes'. The epistatic gene is the gene that does the masking, the hypostatic gene is the gene that gets masked Example seen in labrador coat colour
102
This is just a good way of understanding epistasis :)
There are two genes involved: Gene 1 – B/b B = black pigment b = brown pigment Gene 2 – E/e E = allows pigment to be deposited in fur e = blocks pigment from being deposited 🔗 How they work together: The E gene controls whether pigment shows up at all. If the dog has ee, it can't put pigment in the fur — so it will look yellow, even if it has the black or brown pigment genes
103
What kind of inheritance is Huntington's disease?
Autosomal dominant
104
What are the genetic traits of Huntington's? (frequency, generations)
Appear in both sexes with equal frequency. * Affected individuals have at least one affected parent (unless the mutation has arisen de novo). * Trait does not (generally) skip generations
105
What kind of inheritance is cystic fibrosis?
Autosomal recessive
106
What are the genetic traits of Cystic Fibrosis? (frequency, generations)
Appear in both sexes with equal frequency. * Parents can be unaffected. * Parents are often related, although this depends on the allele frequency in the population. * Trait frequently skips generations.
107
Give 2 examples of X-linked recessive traits and give a brief description of how you can decide whether a trait is X-linked recessive
Red-Green colour blindness and Haemophilia - Appear in males more frequently than females - Parents can be unaffected. - Fathers do not transmit the trait to their sons. - Trait frequently skips generations.
108
Give an example of an X-linked dominant trait
Familial vitamin D-resistant rickets
109
Genetic traits for X-linked dominant familia vitamin D-resistant rickets?
Appear in females more frequently than males * At least one parent affected (unless the mutation has arisen de novo). * Fathers do not transmit the trait to their sons, but do pass it on to all of their daughters. * Trait does not skip generations.
110
Briefly describe how you can tell a trait is X-linked dominant
Appear in females more frequently than males At least one parent affected (unless the mutation has arisen de novo). Fathers do not transmit the trait to their sons, but do pass it on to all of their daughters. Trait does not skip generations
111
What is the nature of the inheritance?
X-linked recessive
112
What is the nature of the inheritance?
Autosomal dominant
113
How do you identify the parental types?
The most common classes
114
What is a gain of function mutation?
Lead to an increased, new, or unregulated function of a gene. Usually dominant – a single mutated copy is enough to show the effect. Example: K-Ras mutations in cancer (RAS oncogene activation).
115
What is a loss of function gene?
Reduce or eliminate the function of a gene. Usually recessive – both copies must be mutated to show the effect. Example: Ras LOF mutations affect differentiation and cell survival in Drosophila.
116
What are the known mutant alleles of a gene and its wild-type allele called?
multiple alleles, or an allelic series.
117
What is the most famous oncogene?
K-Ras Due to gain of function mutations Most are single base missense mutations at G12 G is Glycine, G12D to asparte (D)
118
What are Ras proteins?
Small GTPases that regulate cell growth, proliferation and differentiation, GTP bound active Ras initiates a phosphorylation cascade
119
What does RAS mutations cause?
increases GTP binding - balance is shifted to active state - GTP bound - less hydrolysis due to conformation change - higher affinity for RAF to bind which is activated by RAS - so more signalling
120
Are most gain of function alleles dominant or recessive?
Dominant
121
Are most loss of function alleles dominant or recessive?
Recessive
122
What is the consequence of over-dominance?
The fitness of the heterozygote is higher than the fitness of either homozygote (at least under some conditions, i.e. when there is malaria around) * Sickle cell disease allele is present in the gene pool at higher frequencies than would be expected given the nature of the disease
123
How does sickle cell give an advantage in malaria?
Heterozygote advantage - heterozygous are resistant to malaria with only mild sickle cell symptoms
124
Define pleiotrophy
One gene affects multiple traits - therefore, a single mutation can affect multiple processes - The ability of a single gene to have multiple effects.
125
Why did Mendel use peas?
- They possess different traits - They're protected from foreign pollen as fertilising organs are protected inside - Artificial fertilisation has a high success rate - Self-fertilisation produces a true-breed unless artificial fertilisation is used
126
What is the complementation test?
Used to determine if two mutations are in the same gene
127
If genes do complement what does it show?
No phenotype so mutations are in 2 separate genes
128
If genes fail to complement what does it show?
Phenotype so mutations are of the same gene
129
What is a hypomorph?
partial loss of function allele
130
what is a haplotype?
A group of genes or DNA variations that exist on the same chromosome and are likely to be inherited together.
131
What is an amorph?
complete loss-of-function allele
132
What is hemizygous?
Possessing only one allele of a gene in a diploid cell. All genes on the X chromosome in males are hemizygous
133
Explain the results of a complementation test
If two mutant strains are crossed and the offspring exhibit the wild-type phenotype, then the mutations are in different genes, and complementation has occurred. If the offspring still display the mutant phenotype, then the mutations are likely in the same gene (allelic) and the mutations do not complement
134
What is heterozygous?
Organisms have two different alleles for a particular trait.
135
what is homologous?
Two genes that code for the same type of characteristic. May be homozygous or heterozygous. term used to refer to chromosomes in which one set comes from the male parent and one set comes from the female parent
136
what is homozygous?
organisms that have two identical alleles for a particular trait
137
what is independent assortment?
Random distribution of homologous chromosomes - genes for different traits can segregate independently during the formation of gametes
138
what is linkage?
The case where 2 genes are close together on the same chromosome, such that they do not assort independently in meiosis.
139
What is a transition?
Transitions substitute one purine for the other purine; or one pyrimidine for the other pyrimidine
140
What is a transversion?
Transversions substitute a purine for a pyrimidine or vice versa
141
what is a locus?
Location of a gene on a chromosome
142
What does Hippo do?
It's a tumour supressor gene - more hippo = more cell death
143
what is a mutant?
any organism that has a mutation
144
what is a mutation?
change in DNA sequence
145
what is parental configuration?
the chromosomes found in an offspring that are similar to their parents, same phenotype and alleles
146
what is partial/incomplete dominance?
A gene pair in which neither allele is dominant and the heterozygous individuals express both alleles and display an intermediate phenotype.
147
what is penetrance?
The percentage of individuals with a specific genotype who also express the expected phenotype
148
what is a phenotype?
physical characteristics of an organism
149
what is a propositus/proband?
the family member chosen as the starting point in genealogical research, in the investigation of an inheritable disease, etc. - may have genetic therapy
150
what is a recessive allele?
An allele that is masked when a dominant allele is present
151
what is a recombinant?
any organism that contains genes that originated in another organism
152
what is recombination?
the rearrangement of genetic material, especially by crossing over in chromosomes or by the artificial joining of segments of DNA from different organisms.
153
what is self fertilisation?
When a plant pollinates its own flower.
154
How does epistasis affect gene interactions?
Any time two different genes contribute to a single phenotype and their effects are not merely additive, those genes are said to be epistatic
155
what is a sex chromosome?
a chromosome involved with determining the sex of an organism, typically one of two kinds. X and Y
156
what is a test cross?
cross between an organism with an unknown genotype and an organism with a recessive phenotype - crossing an organism with a dominant phenotype with one that has a recessive phenotype
157
What is Transmission genetics?
how genes are transmitted from parents to offspring - How and what traits can be inherited - Is gene inherited - How gene is inherited - How genes recombine - What are the locations of genes in the genome
158
What is molecular genetics?
- What the molecular nature of genetic material is - How genes control life functions
159
Define incomplete penetrance
Not every individual with the genotype expresses the corresponding phenotype
160
What is population genetics?
- How different forms of genes (alleles) are distributed in populations
161
What is evolutionary genetics?
- How genes change in a population over time
162
what is P0?
parental generation
163
what is chi-squared test?
A statistical test to find out whether the difference between observed and expected data is due to chance or a real effect.
164
equation for chi-squared test?
X2 = ∑ ((o-e)2/e)
165
what is genetic mapping?
The process of determining the location and chemical sequence of specific genes on specific chromosomes. can also map new mutations
166
what is the positive gene/ plus gene?
the donor gene
167
When do we accept/fail to reject null hypothesis?
When P>0.05
168
When do we reject null hypothesis?
When P<0.05
169
What does it mean if we reject the null hypothesis?
There is a significant difference at 0.05% and results aren't due to chance
170
What does it mean if we accept/ fail to reject null hypothesis?
There isn't a significant difference at 0.05% and results are due to chance
171
What is complete monosomy?
Missing a whole chromosome
172
what is aneuploidy?
Abnormal number of chromosomes du eta nondisjunction in meiosis
173
What is nondisjunction?
Chromosomes not segregated at 2nd division so get double DNA in one cel and not the other
174
What were the key findings from Morgans fly experiment?
- Sex linked genes are carried on the X chromosome - Male inherit X from mother and Y from father - females inherit an X from each parent - Y chromosome carries few genes - Males are homozygous for X chromosome (only one copy of it)
175
What did the first mapping of X chromosome show?
Genes are in a linear order on the chromosome. – They are in the same position in all individuals
176
What ratio does incomplete dominance give?
1:2:1
177
What can we use pedigree analysis for?
Identifying mutant alleles underlying human disorders - predict if child will inherit disorder - know if its autosomal or x-linked and if dominant or recessive
178
Are mendelian traits linked?
No they're not on the same chromosome
179
How can you find which genes a mutation works with?
Once isolated mutation and mapped it to a gene can use: - educated guess - screens - biochemical binding partners - seeing how it changes a phenotype
180
How can you use a modifier screen to find which gene a mutation works with?
1. must start with an obvious phenotype 2. establish a tester stock (small wings) 3. cross mutagenise males to virgins from tester stock 4. screen for modifiers (other tumour suppressor genes) 5. map new mutation when see genetic interaction
181
What tumour suppressor is epistatic to hippo?
Warts tumour suppressor
182
What is incomplete penetrance caused by? which also causes variable expressivity
1. Interacting genes in the rest of the genome - modifiers, epistatic genes or suppressors 2. influence of environment
183
what is expressivity?
Measure the intensity of a phenotype - can get variable expressivity
184
if two genes are on two different chromosomes, will they assort independently of each other or not?
They assort independently of each other, not linked
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