Genetics 2

Question 1

Recombination:

Answer 1

production of new allele combinations

Question 2

Independent assortment of genes at meiosis

Answer 2

interchromosomal recombination
major means by which organisms produce new combinations of allels

Question 3

Recombinant:

Answer 3

Any meiotic product that has a new combination of the alleles provided by the
two input genotypes

Question 4

Meiotic recombination:

Answer 4

is any meiotic process that generates a haploid product with new
combinations of the alleles carried by the haploid genotypes that united to form the meiocyte

Question 5

Haploids (single set of chromosome in each cell)

Recombinants are meiotic output different from meiotic input.

Answer 5

This is because meiotic input is the genotype of individuals (haploid since meiosis) and and the meiotic output is the two parental inputs (meiotic input) along with the recombinants

e.g., AB + ab (inputs)

meiotic diploid = AaBb

output (from crossing with itself) = AB, ab, aB, Ab

Question 6

Diploids (2 sets of chromosomes in each cell)

recombinants
are best detected in a testcross

Answer 6

Input and output are gametes (reproductive cells)

-To know input gametes: pure breeding parents
e.g., AABB + aabb

INPUTS = AB + ab

-To detect recombinant output gametes:
testcross and observe progeny

meiotic diploid = AaBb

cross with test cross (aabb)

output are the F2 and will include the parental genotypes with the recombinants

Question 7

Recombinant frequency (RF):

Answer 7

The proportion (or percentage) of recombinant cells or individuals

• A recombination frequency of 50% indicates
  that the genes are independently assorting
  and are most likely on different chromosomes

Question 8

Diagnostics of Linkage

Answer 8

-When two genes are close together on the same chromosome pair (that is, when they are
Linked), they do not assort independently but produce a recombinant frequency of less than 50 Percent.
Hence, a recombinant frequency of less than 50 percent is a diagnostic for linkage

Question 9

Two types of meiotic recombination

Answer 9

Interchromosomal recombination:
Recombination by Mendelian independent assortment (RF = 50%)

● Intrachromosomal recombination:
Crossing over (RF < 50%)
- Homologous recombination – molecular mechanism of crossing ove

Question 10

Homologous recombination – molecular mechanism
of crossing over

Answer 10

-For linked genes, recombinants are produced by crossovers between nonsister chromatids during meiosis

-When homologous chromosomes pair at
meiosis, the chromosomes occasionally
break and exchange parts in a process
called crossing over.

• A cross-shaped
  structure called a chiasma (pl., chiasmata)
  often forms between two nonsister
  chromatids.

Question 11

Chromosome map:

Answer 11

shows unidirectional arrangement of genes on a chromosome
Gene Position on a chromosome known as locus

-2 types of maps:

● Recombination-based maps: map of genes identified by mutant phenotype showing single gene inheritance. Recombination maps are generated with linkage analysis
● Physical Maps: genes as segments along DNA of chromosome

Question 12

Three-point testcross

Answer 12

● cross of a trihybrid (triple heterozygote) with a triply recessive tester
● deduce whether three genes are linked, if so deduce their order and distances between them

Question 13

Linkage Symbolism and Terminology

Answer 13

-cis = AB/ab or ++/ab (dominant alleles on the same homolog)
-trans = dominant alleles on opposite homolog Ab/aB or

• alleles are always written in the same order on each homolog
  -slash separates the two homologs for linked alleles
  -semi colon separates the two homologs for unlinked alleles A/a;B/b
  -period separates two homologs for alleles with unknown linkage A/a . B/b

Question 14

Heteroduplex DNA

Answer 14

-DNA THAT CONTAINS TWO COMPLIMENTARY strands of dna that originated front different homologs

Question 15

Using ratios as diagnostics

(come back)

Question 16

iNTERFERENCE

Answer 16

I = 1 - coc

c.o.c = observed number of double recombinants/expected number of double recombinants

observed = total number of double recombinants (sum)

expected = percentage of each double recombinant multiplied together and then multiplied with the total progeny

I = 0 : no interference between two crosses (crossovers occur independently)

If I = 1, then interference is complete. No double crossovers occur.

Question 17

Allelic series

Answer 17

Known mutant alleles of a gene and its WT allele

Question 18

Full, or complete dominance:

Answer 18

when the homozygous dominant cannot be distinguished from the
heterozygote at the phenotypic level.

-Fully dominant allele is expressed when only one copy is present (as in a heterozygote),
whereas the other allele is fully recessive

-

Question 19

Functional Effects of Mutation

Answer 19

• Loss-of-function: alleles that result in a significant decrease (hypomorphic/leaky mutation) or in the
  complete loss (amorphic/null mutation) of the functional activity of a gene product.
• Gain-of-function: alleles that have acquired a new function (neomorphic mutation) or have their expression altered in a way that gives them substantially more activity than the wild-type allele (hypermorphic mutation)

Any heterozygote containing the new allele along with the original wild type allele will express the new allele. Genetically this will define the mutation as a dominant.

Recessive mutations are usually loss-of-function mutations (haplosufficiency).

Dominant mutations can be gain-of-function, dominant negative, or loss-of-function (in the case of haploinsufficiency).

Question 20

iNCOMPLETE dOMINANCE

Answer 20

• First, Cross: 2 pure breeding lines
  P: A/A (WT, red) x a/a (mutant, white petals)

F1 = The phenotype of a heterozygote is intermediate between those of the two homozygotes, on some quantitative scale of measurement = PINK

• sELF THE F1

1:2:1 (2 A alleles = red, 1 A allele = pink, 0 A allele = white)

Question 21

Codominance

Answer 21

-both phenotypes expressed with equal dominance

e.g., blood groups
IA and IB alleles together express AB sugar and they are dominant to i (i alone doesn’t exress anything and paired with one of them, it is recessive)
i = null allele since ii = no A or B and gives O
IA IA = A
IA i = A
IB IB = B
IB i = B

Question 22

Recessive lethal alleles

Answer 22

• allele capable of causing death of an organism

AY allele: yellow coat color
A allele: WT, brown (Agouti)

Cross1: AY/A (yellow) x A/A (WT)
F1 = 1 : 1 ratio AY/A (yellow) : A/A (WT)

• self them
  AY/A (yellow) x AY/A (yellow)

Viable F2 = 2:1

2/3 AY/A (yellow)
1/3 A/A (WT)

Because …
¼ A/A WT
½ AY/A yellow
¼ AY/AY lethal
AY/AY = lethal in homozygous state

Question 23

Pleiotropic:

Answer 23

allele that affects more than one property of an organism

e.g., lethal alleles since they effect viability and fur colour

Question 24

Type of Lethal alleles

Answer 24

Recessive lethal:
- mutant allele causes death when homozygous.
-can code for dominant or recessive traits in the heterozygous state

Dominant lethal:
one copy of the mutant allele results in death
-Rarely observed; inherited and
present in the population only if lethality happens later in life

Conditional lethal:’
-viable in one environment and lethal in another

Question 25

Variability in Phenotypes

Answer 25

Penetrance: percentage of individuals with a given allele who exhibit the phenotype associated with that allele. Expressivity: degree to which a given allele is expressed at the phenotypic level; i.e. intensity of phenotype

Question 26

complementation test

Answer 26

for diploids to test if two mutants with same phenotype are allelic or whether the mutations are in different genes: 1) cross 2 individuals homozygous for different recessive mutations 2) If progeny shows the wild-type phenotype, the two recessive mutations must be in different genes because the respective WT alleles provide WT function, i.e. in this case we say the mutations have complemented each other 3) If progeny does not have wild-type phenotype but shows the mutant phenotype(s) then they do not complement and the initial recessive mutations must be allelic, i.e. different mutants of same gene.

Question 27

Complementation:

Answer 27

the production of a wild-type phenotype when two haploid genomes bearing different recessive mutations are united in the same cell.

Question 28

Inferring gene interactions

Answer 28

- Complementation Test -If mutants are in different genes,combine the different mutants in pairs to form double mutants: -Double mutant is obtained by crossing two homozygous recessive single mutants and selfing the F1 -Assess F2 for 9:3:3:1 which gives different types of gene interactions

Question 29

Types of gene interactions

Answer 29

-9:3:3:1 = no gene interaction 9 a+/-;b+/- 3: a+/-;b/b 3 a/a;b+/- 1 o/o;b/b -9:3:3:1 -> 9(WT):7(mutant) = complementary gene action (The wild-type action from both genes is required to produce the wild- type phenotype. Mutation of one or both genes produces a mutant phenotype) -9:3:3:1 -> 15(wt):1(mutant) = duplicate gene action (allows dominant alleles of either duplicate gene to produce the wild-type phenotype. Only organisms with homozygous mutations of both genes have a mutant phenotype e.g., pprr since dominant is P and R) -9:3:3:1 -> 9:6:1 = dominant gene interaction (occurs between genes that each contribute to a phenotype, producing one phenotype if dominant alleles are present at each gene, a second phenotype if recessive alleles are homozygous for either gene, and a third phenotype if recessive homozygosity occurs at both genes)

Question 30

Epistasis

Answer 30

when a mutant allele of one gene masks the expression of a mutant allele of another gene and expresses its own phenotype instead.

Question 31

recessive epistasis

Answer 31

Recessive epistasis occurs when recessive alleles at one gene (gene 2) mask or reduce the expression of alleles at the interacting locus (gene 1) -9:3:4

Question 32

dominant epistasis

Answer 32

a dominant allele of one gene masks or reduces the expression of alleles of a second gene -9:3:3:1 -> 12:3:1

Question 33

Suppressors

Answer 33

Suppressor: mutant allele of a gene that reverses the effect of a mutation of another gene, resulting in wild-type or almost wild-type phenotype Revertant: reversal of the original mutation that results in WT phenotype

Question 34

recessive suppressor that has no phenotype

Answer 34

13:3

Question 35

Synthetic lethals

Answer 35

Two mutations that are individually benign can become lethal when united in the same genotype. F2 = 9:3:3 -double mutant = 1 and is absent

Question 36

Transposable Elements (transposons)

Answer 36

- Genetic loci that can move from one location in the genome to another.

Question 37

Transposition

Answer 37

A process by which mobile genetic elements move from one location in the genome to another.

Question 38

Back cross

Answer 38

crossing of hybrid with parent

Question 39

Activator (Ac) and Dissociation (Ds

Answer 39

- Transposable elements in maize can inactivate a gene in which they reside, cause chromosome breaks, and transpose to new locations within the genome. - Autonomous elements can perform these functions unaided; - nonautonomous elements can transpose only with the help of an autonomous element elsewhere in the genome.

Question 40

Transposase:

Answer 40

An enzyme encoded by transposable elements that undergo conservative transposition.

Question 41

Nonautonomous transposable element

Answer 41

- A transposable element that relies on the protein products of autonomous elements for its mobility. - Dissociation (Ds) is an example of a nonautonomous transposable element.

Question 42

Autonomous transposable element:

Answer 42

- A transposable element that encodes the protein(s)—for example, transposase or reverse transcriptase—necessary for its transposition and for the transposition of nonautonomous elements in the same family. - Ac is an example of an autonomous transposable element.

Question 43

Insertion Sequence (IS) Element

Answer 43

A mobile piece of bacterial DNA (several hundred nucleotide pairs in length) capable of inactivating a gene into which it inserts. -IS elements have inverted repeat sequences (IR) which are identical sequences but inverted -Structure of IS elements = transposase gene with Inverted repeats on each end

Question 44

Composite transposon

Answer 44

A type of bacterial transposable element containing a variety of genes that reside between two nearly identical insertion-sequence (IS) elements

Question 45

Simple transposons:

Answer 45

A type of bacterial transposable element containing a variety of genes that reside between short inverted repeat sequences

Question 46

two stages of transposition

Answer 46

excision (leaving) from the original location, and insertion into the new location.

Question 47

Replicative transposition (“copy and paste”)

Answer 47

- Replicative transposition: A mechanism of transposition that generates a new insertion element integrated elsewhere in the genome while leaving the original element at its original site of insertion. - Cointegrate: The product of the fusion of two circular elements to form a single, larger circle in replicative transposition

Question 48

Conservative transposition (“cut and paste”

Answer 48

Conservative transposition: A mechanism of transposition that moves a mobile element to a new location in the genome as it removes that element from its previous location

Question 49

Target-site duplication:

Answer 49

A short direct-repeat DNA sequence (typically from 2 to 10 bp in length) adjacent to the ends of a transposable element that was generated during the element’s integration into the host chromosome.

Question 50

Transposable elements in eukaryotes

Answer 50

● Class 1 transposable elements: retrotransposons ● Class 2 transposable elements: DNA transposons

Question 51

Retrotransposons (come back)

Answer 51

A transposable element that uses reverse transcriptase to transpose through an RNA intermediate

Question 52

Aberrant Euploid

Answer 52

when a cell has more or less than the normal number of chromosome sets

Question 53

Aneuploid

Answer 53

organism gains or loses one or more chromosomes, but not a complete set (“not euploid”). The chromosome number of aneuploids is not an exact multiple of the haploid number, n

Question 54

Aberrant euploidy

Answer 54

-Monoploids: individual of a normally diploid species that has one chromosome set -In most species monoploids are not viable. They carry a number of recessive lethal alleles. The total set of deleterious alleles is called a genetic load. The deleterious alleles are masked by the WT alleles in the diploid condition, but would be expressed as a monoploid -Monoploid individuals cannot undergo meiosis successfully because the single chromosome set has no pairing partners for meiosis I. Monoploids are sterile Polyploids Very common in plants, rare in animals. Often associated with origin of new species. In aberrant euploids: there is often a positive correlation between the number of copies of a chromosome set and the size and vigor of an organism (i.e. polyploids are often larger and have larger component parts than their diploid relatives). Higher ploidy produces larger size (e.g., 8n = large vs 2n = small)

Question 55

Triploids (3n)

Answer 55

-2n +n -2n + 4n -Typically seen in plants, not animals -pairings = trivalent (pair plus one) or univalent (unpaired homolog) plus a bivalent (paired homolog) -Polyploids with odd numbers of chromosome sets, such as triploids, are sterile or highly infertile because their gametes and thus their offspring are aneuploid (usually becomes inviable)

Question 56

Reciprocal translocations

Answer 56

Genetic consequences of reciprocal translocations: ● semi sterility ● pseudolinkage of genes known to be on different chromosomes ● alterations in chromosome size

Question 57

Types of Polyploids

Answer 57

* Autopolyploidy (auto = self): multiple chromosome sets from same species. The differentchromosome sets would be fully homologous since they originated from the same species. * Allopolyploidy (allo = different): chromosome sets from two different but very closely related species. The different chromosomes sets in the polyploid species would be homeologous (partly homologous)

Question 58

Inversions

Answer 58

The main diagnostic features of heterozygous inversions are: ● inversion loops ● reduced recombinant frequency ● reduced fertility because of nonviable gametes

Question 59

Balanced rearrangements

Answer 59

- A change in the chromosomal gene order that does not remove or duplicate any DNA. - The two classes of balanced rearrangements are inversions and reciprocal translocations

Question 60

Deletions

Answer 60

- Deletion of a segment on one homolog sometimes unmasks recessive alleles present on the other homolog leading to their unexpected expression. - Pseudodominance: the appearance of a recessive phenotype due to the deletion of masking dominant allele(s)

Question 61

Nondisjunction

Answer 61

- a failure of normal segregation of homologs to opposite poles at meiotic or mitotic division - Crossovers are needed to keep bivalents paired until anaphase I. If crossing over fails, first-division nondisjunction occurs.

Question 62

Aneuploidy in humans

Answer 62

Trisomy (2n+1) (n + 1) gamete + n gamete = 2n +1 zygote (trisomic) Trisomics contain an extra copy of one chromosome. In diploids, frequently results in abnormality or death, autosomal trisomies are mostly lethal in animals Trisomy XXY (Klinefelter syndrome) Phenotypic males. Sterility as a consequence of altered development. Trisomy XYY Fertile male: X pairs with only one Y. Other Y does not pair at meiosis I and is not transmitted to gametes (i.e. X or Y gametes, not XY or YY)**. Trisomy XXX (Triple X Syndrome) Phenotypically normal, fertile female. At meiosis only two X pair, third X does not pair and is not transmitted to gametes (i.e. X gametes, not XX)**.