Exam 1 Flashcards
ploidy
Ploidy is the number of complete sets of chromosomes in a cell or organism.
haploid number
The haploid number refers to the number of unique chromosomes in a single set of chromosomes for a particular species.
homologous chromosome
A homologous chromosome is one of a pair of chromosomes that have the same genes at the same positions and the same centromere locations.
allele
An allele is one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.
Understand that mitotic division does not change ploidy
Describe basics of sexual reproduction – germ cells, gametes, fertilization
Germ cells undergo meiosis to produce haploid gametes (sperm and eggs). During fertilization, a haploid sperm cell fuses with a haploid egg cell, combining their chromosomes to form a diploid zygote. This restores the original ploidy of the organism in the zygote and subsequent cells formed by mitotic divisions during development.
Understand why meiosis is needed to create gametes (why mitosis cannot be used to
create gametes)
Mitosis cannot be used to create gametes because it maintains the same ploidy in daughter cells. Meiosis is required to halve the ploidy and produce haploid gametes, so that fertilization restores the original diploid ploidy.
Describe the phases of meiosis
Meiosis I:
Prophase I - Chromosomes condense, homologous chromosomes pair up.
Metaphase I - Paired homologous chromosomes line up along the center.
Anaphase I - Homologous chromosomes separate and move to opposite poles.
Telophase I - Chromosomes arrive at poles, nuclear membranes reform around each set.
Meiosis II:
Prophase II - Chromosomes condense again.
Metaphase II - Chromosomes line up individually.
Anaphase II - Sister chromatids separate and move to opposite poles.
Telophase II - Haploid daughter cells form with one chromosome set each.
Understand that meiosis separates homologous chromosome, which separates alleles of the same gene apart
During meiosis, the separation of homologous chromosomes in Anaphase I is what allows different combinations of alleles for each gene to be distributed into the resulting gametes. Since homologous chromosomes carry different versions (alleles) of the same genes, separating the homologous pairs ensures that each gamete receives a unique mixture of maternal and paternal alleles. This genetic reshuffling by separating homologous chromosomes is a key reason meiosis generates genetic diversity in gametes and offspring.
Be able to describe crossing over and independent assortment in meiosis
Crossing over: Exchange of genetic material between homologous chromosomes during prophase I.
Independent assortment: Random segregation of maternal and paternal chromosomes into gametes during anaphase I.
Both crossing over and independent assortment generate genetic diversity in gametes produced by meiosis.
Understand how crossing over and independent assortment can create unique gametes
Crossing over: By exchanging chromosome segments between homologous pairs, new combinations of maternal and paternal genes are created on each chromosome.
Independent assortment: The random segregation of chromosomes into gametes means each gamete will get a unique assortment of maternal and paternal chromosomes.
The combined effects of recombination from crossing over and the randomized chromosome assortment means that out of the millions of possible gametes, virtually every one receives a different complement of genes and alleles. This genetic uniqueness of gametes facilitates greater diversity in offspring produced by sexual reproduction.
gamete
A gamete is a haploid reproductive cell that fuses with another during fertilization in sexual reproduction.
fertilization
Fertilization: The fusion of two gametes (egg and sperm) to form a diploid zygote.
crossing over
Crossing over: The exchange of genetic material between homologous chromosomes during meiosis, which generates new combinations of maternal and paternal genes.
independent assortment
Independent assortment: The random segregation of maternal and paternal chromosomes into gametes during meiosis.
tetrad
Group of four chromatids/haploid cells held together after meiosis II
homologous pair
Two chromosomes in a diploid cell that carry genes for the same traits
One chromosome from each parent
Pair up and exchange genetic material during meiosis
synaptonemal complex
Synaptonemal complex:
- Protein structure that forms between homologous chromosomes during prophase I of meiosis
- Facilitates crossover events and recombination between non-sister chromatids
- Helps hold homologous pairs together until separation in anaphase I
cohesin
Cohesin:
- Protein complex that holds sister chromatids together after DNA replication
- Ensures proper separation of sister chromatids during anaphase of mitosis and meiosis
- Removed from chromosomes in a regulated manner to allow segregation
chiasma/chiasmata
Chiasma/Chiasmata:
- The point(s) where crossing over occurs between non-sister chromatids of homologous chromosomes
- Physically holds chromatids together until anaphase I of meiosis
- Singular: chiasma, plural: chiasmata
- Allows for genetic recombination and increased genetic diversity
sister chromatid
Sister chromatids:
- Two identical copies of a chromosome formed after DNA replication
- Held together by the cohesin protein complex until anaphase
- Separate and migrate to opposite poles during anaphase of mitosis and meiosis II
- Genetically identical unless a new mutation occurs
cell cycle
Cell cycle:
- Sequence of events that take place in a cell leading to its division and duplication
- Consists of interphase (G1, S, G2 phases) and M phase (mitosis)
- Regulated by cyclin-dependent kinases and checkpoints
- Ensures proper division and genetic distribution to daughter cells
interphase
Interphase:
- Longest phase of the cell cycle
- Consists of G1, S, and G2 phases
- Cell grows, duplicates organelles and chromosomes (during S phase)
- Prepares for mitosis or meiosis
- Most metabolic activity occurs during interphase
Describe the characteristics and feature of Mendelian traits
Here are the key characteristics of Mendelian traits in concise bullet points:
- Determined by discrete units (genes)
- Dominant and recessive alleles
- Alleles segregate during gamete formation
- Independent assortment of traits
- Simple dominance (one allele masks the other)
- Predictable phenotypic ratios in offspring
- Can be monohybrid (single trait) or dihybrid (two traits)
Explain dominance (allelic relationship) and complete dominance
Dominance (allelic relationship):
- Refers to the expression of one allele over another in a heterozygous genotype
- Complete dominance: When the phenotype of the heterozygous genotype is indistinguishable from one of the homozygous genotypes
- Example: In pea plants, tall (TT or Tt) is completely dominant over short (tt)
- Incomplete dominance: When the heterozygous phenotype is distinct from both homozygous phenotypes
- Example: In snapdragons, red (CR) and white (CW) produce pink flowers (CRCw)
Understand the consequence of segregation, ind. assortment, and crossing over when
considering one gene
When considering a single gene, here are the consequences of segregation, independent assortment, and crossing over:
Segregation:
- During gamete formation, the two alleles for a gene separate or segregate
- This leads to gametes receiving only one allele for that gene
- Consequence: Offspring receive one allele from each parent, enabling genetic variation
Independent Assortment:
- For a single gene, independent assortment does not have an effect
- Independent assortment applies when considering two or more genes on different chromosomes
Crossing Over:
- Crossing over involves the exchange of genetic material between non-sister chromatids of homologous chromosomes
- For a single gene, crossing over can result in new combinations of alleles on the same chromosome
- Consequence: Increases genetic variation by creating new allele combinations in gametes
In summary, for a single gene:
- Segregation ensures offspring receive different allele combinations from parents
- Crossing over can create new allele combinations on the same chromosome
- Independent assortment is not applicable for a single gene
histone
Histone:
- Small, highly conserved proteins found in eukaryotic cell nuclei
- Act as spools around which DNA winds to form nucleosomes
- Help package and order the DNA into structural units called chromatin
- Play a role in gene regulation by controlling access to DNA
- Core histones: H2A, H2B, H3, H4 form nucleosome core particle
- Histone tails can be modified (e.g. acetylation, methylation) affecting gene expression
nucleosome
Nucleosome:
- Basic structural unit of chromatin
- Consists of a histone core around which DNA is wrapped
- Histone core is an octamer of histone proteins (2 copies each of H2A, H2B, H3, H4)
- Around 147 base pairs of DNA wrapped around the histone core
- Connected by short stretches of linker DNA and linker histones
- Allows compaction of DNA into higher-order chromatin structures
- Regulates access of enzymes/transcription factors to DNA
chromatin
Chromatin:
- Complex of DNA and proteins that condenses to form chromosomes
- Found in the nucleus of eukaryotic cells
- Basic unit is the nucleosome (histone core + wrapped DNA)
- Allows compaction of long DNA molecules into smaller structures
- Exists in two forms:
- Euchromatin (less condensed, transcriptionally active)
- Heterochromatin (highly condensed, transcriptionally inactive)
- Structure and modifications regulate gene expression
- Chromatin remodeling alters chromatin structure for DNA access
uncondensed/condensed chromatin
Uncondensed chromatin refers to loosely packed DNA, allowing for transcription and gene expression. Condensed chromatin is tightly packed DNA, often associated with inactive genes and during cell division.
dominant
In genetics, “dominant” refers to an allele that will manifest its phenotype when present, masking the effect of its recessive counterpart in a heterozygous individual.
recessive
In genetics, “recessive” refers to an allele whose phenotypic expression is masked by a dominant allele when present in a heterozygous individual. It typically manifests its phenotype only when present in a homozygous recessive genotype.
phenotype
The “phenotype” refers to the observable traits or characteristics of an organism, resulting from the interaction of its genetic makeup (genotype) with the environment. These traits can include physical features, biochemical properties, and behaviors.
genotype
The “genotype” refers to the genetic makeup of an organism, including the combination of alleles present at specific loci on its chromosomes. It represents the genetic information that determines an organism’s traits and characteristics.
homozygous
“Homozygous” refers to an individual having identical alleles at a particular gene locus on both homologous chromosomes. In other words, both alleles at a specific gene locus are the same (e.g., AA or aa).
heterozygous
“Heterozygous” refers to an individual having different alleles at a particular gene locus on homologous chromosomes. In other words, the alleles at a specific gene locus are different (e.g., Aa).
law of segregation
The “law of segregation” is a principle in genetics formulated by Gregor Mendel. It states that during the formation of gametes (sex cells), the two alleles for each gene segregate from each other so that each gamete carries only one allele for each gene. This segregation occurs randomly and independently of alleles at other gene loci.
crossing over
“Crossing over” is a genetic process that occurs during meiosis, specifically during prophase I of meiosis I. It involves the exchange of genetic material between homologous chromosomes, resulting in the recombination of alleles. Crossing over increases genetic diversity by creating new combinations of alleles on chromosomes.
allelic relationship (dominance)
Allelic relationship, specifically dominance, refers to the interaction between alleles of a gene when present in a heterozygous individual. In a dominant-recessive allelic relationship, the dominant allele expresses its phenotype, masking the effect of the recessive allele. The dominant allele is fully expressed, while the recessive allele’s phenotype is only observed when present in a homozygous recessive state.
complete dominance
Complete dominance: Phenotype of heterozygote identical to homozygous dominant.
Differentiate sister chromatids vs. homologous chromosomes – be able to tell if sister or homolog or non-homologous given particular information about alleles or meiotic structures
Sister chromatids: Identical copies of a single chromosome resulting from DNA replication.
Homologous chromosomes: Chromosome pairs from each parent, similar in length and gene position but may carry different alleles.
To differentiate:
- Sister chromatids are identical copies.
- Homologous chromosomes are from different parents and may have different alleles.
During meiosis:
- Sister chromatids are present in both meiosis I and meiosis II.
- Homologous chromosomes pair up only in meiosis I.
Differentiate DNA condensation phases interphase vs. M phase
Interphase: DNA exists as chromatin, loosely packed for gene expression and replication.M phase: DNA condenses into visible chromosomes for accurate segregation during cell division.
Understand Mendelian gene rules + complete dominance definition and how to identify if complete dominance is occurring.
Mendelian gene rules:
1. Law of Segregation: During gamete formation, the two alleles for each gene segregate from each other so that each gamete carries only one allele for each gene.
2. Law of Independent Assortment: Alleles for different genes segregate independently of each other during gamete formation.
Complete dominance definition:
Complete dominance occurs when the phenotype of the heterozygous genotype is indistinguishable from that of the homozygous dominant genotype. In other words, one allele completely masks the effect of the other allele in a heterozygous individual. The dominant allele is fully expressed, while the recessive allele has no observable effect on the phenotype.
Identifying complete dominance:
To identify complete dominance, observe the phenotype of heterozygous individuals. If the phenotype of the heterozygote is identical to that of the homozygous dominant individual, complete dominance is occurring. In other words, if there is no visible difference between the heterozygote and the homozygous dominant individual, complete dominance is likely at play.
Comprehend how crossing over and independent assortment impact the possible gamete genotypes and frequencies when only ONE gene.
Crossing over: Exchange of genetic material between homologous chromosomes during meiosis, creating new combinations of alleles for one gene.Independent assortment: Alleles for different genes segregate independently during gamete formation, leading to different combinations of alleles for one gene in gametes.Impact: Increases genetic diversity among gametes by generating new allele combinations, contributing to variability in offspring.
Know how to find the probabilities of a genotype/phenotype when given the parent’s genotype/phenotype or other information
To find genotype or phenotype probabilities:
- Identify parent genotypes.
- Use Punnett square to visualize offspring genotypes.
- Count squares for each genotype.
- Divide by total squares for genotype probabilities.
- Adjust for phenotype probabilities based on genotype-phenotype relationship or additional information.
Monohybrid Cross with Complete Dominance Refresher - Know the genotype and phenotype ratios
In a monohybrid cross with complete dominance, where one allele completely masks the effect of the other allele, the genotype and phenotype ratios in the offspring are predictable.
Genotype ratio:
- 1 homozygous dominant : 2 heterozygous : 1 homozygous recessive
Phenotype ratio:
- 3 individuals showing the dominant phenotype : 1 individual showing the recessive phenotype
This ratio follows the Mendelian principles of inheritance, specifically the law of segregation and complete dominance, where the dominant allele masks the expression of the recessive allele in heterozygous individuals.
Refresh genes, alleles, central dogma, and mutation
Genes: DNA segments with instructions for traits.
Alleles: Different gene versions.
Central Dogma: DNA to RNA to protein flow.
Mutation: DNA sequence change.
Understand how genotype produces phenotype in terms of protein function - Biallelic expression - Loss of function (lof) vs. gain of function (gof) mutants
Genotype to Protein: Genes (genotype) encode instructions for protein synthesis. Through transcription and translation, mRNA is produced and translated into proteins.Protein Function: Proteins perform various functions in the cell, such as enzymatic activity, structural support, or signaling. The specific function of a protein determines the phenotype.Biallelic Expression: In biallelic expression, both alleles contribute to the phenotype. If one allele is mutated (e.g., LOF or GOF), it affects protein function and thus the phenotype.Loss of Function (LOF) Mutants: LOF mutations result in a protein with reduced or abolished function. This can occur through various mechanisms such as premature stop codons, altered protein folding, or disrupted binding sites. As a result, the phenotype may show a loss or reduction of the protein’s normal function.Gain of Function (GOF) Mutants: GOF mutations lead to a protein with new or enhanced functions. This can arise from mutations that increase protein activity, alter protein interactions, or confer novel properties. GOF mutations can result in abnormal phenotypes due to the altered protein function.
monohybrid
A monohybrid refers to a genetic cross involving only one trait, typically governed by one gene with two different alleles. In a monohybrid cross, individuals with different alleles for the same gene are crossed to study the inheritance pattern of that specific trait.
mutant/variant
“Mutant” and “variant” are terms used in genetics to describe alterations or differences in the DNA sequence compared to a reference or wild-type sequence.
- Mutant: A mutant refers to an organism or cell with a genetic mutation, which is a permanent change in the DNA sequence. Mutations can arise spontaneously or be induced by external factors like radiation or chemicals. Mutations can result in changes to an organism’s traits or characteristics.
- Variant: A variant refers to a version or form of a gene or DNA sequence that differs from the reference or wild-type sequence found in most individuals of a species. Variants can be natural variations within a population or population-specific differences. Variants may or may not have a discernible effect on phenotype, and they can be benign or pathogenic depending on their impact on protein function or gene regulation.
silent mutation
A silent mutation is a DNA change that doesn’t alter the amino acid sequence of a protein.
missense mutation
A missense mutation is a type of mutation that occurs in a DNA sequence, resulting in the substitution of one amino acid for another in the corresponding protein. Unlike silent mutations, which do not change the amino acid sequence, missense mutations lead to the production of a protein with a different amino acid at one position. Depending on the specific amino acid change and its location within the protein, missense mutations can have varying effects on protein structure and function. They can range from being benign with little or no effect to causing significant alterations in protein activity or stability, potentially leading to changes in the phenotype of the organism.
nonsense mutation
A nonsense mutation is a type of mutation that occurs in a DNA sequence, resulting in the premature termination of protein synthesis. This happens when a codon that normally codes for an amino acid is changed to a stop codon (e.g., UAA, UAG, or UGA). As a result, translation of the mRNA molecule is terminated prematurely, leading to the production of a truncated, nonfunctional protein. Nonsense mutations often result in loss of protein function and can lead to genetic disorders or diseases, depending on the specific gene affected and its role in cellular processes.
Understand how to determine complete vs. incomplete vs. co-dominance
* Which genotype’s phenotype matters??
Determining complete vs. incomplete vs. co-dominance involves understanding how alleles interact:
- Complete dominance: Only the dominant allele’s phenotype matters.
- Incomplete dominance: Phenotype is a blend of both alleles.
- Co-dominance: Both alleles’ phenotypes are expressed equally.
Connect protein function to incomplete and co-dominance
In incomplete dominance and co-dominance:
- Incomplete: Heterozygotes show an intermediate phenotype, suggesting partial protein function from both alleles.
- Co-dominance: Heterozygotes express both alleles fully, indicating separate and simultaneous protein functions.
Understand what multiple allelism is and why it might result in more than one dominance rule used for alleles
Multiple allelism: Presence of more than two alleles for a gene.
Results in varied dominance rules due to specific interactions between alleles.
Know the difference between autosomes vs. sex chromosomes as well as autosomal genes vs. sex-linked genes
Autosomes vs. Sex Chromosomes:
- Autosomes: Non-sex determining chromosomes (pairs 1 to 22).
- Sex Chromosomes: Determine an individual’s sex (X and Y in humans).
Autosomal Genes vs. Sex-linked Genes:
- Autosomal Genes: Located on autosomes, follow Mendelian inheritance.
- Sex-linked Genes: Located on sex chromosomes, show different inheritance patterns between males and females.
Know that X and Y chromosomes, despite having PAR, are not called homologous
Describe pleiotropy
Pleiotropy is a phenomenon in genetics where a single gene affects multiple, seemingly unrelated phenotypic traits. In other words, a mutation in one gene can lead to the expression of multiple phenotypic characteristics, which may appear unrelated at first glance. This can occur because genes often code for proteins with multiple functions or are involved in multiple biochemical pathways within the cell. Pleiotropy can have significant implications for the understanding of genetic disorders and the development of traits in organisms.
multiple allelism (multiple alleles),
Multiple allelism: Presence of more than two allelic forms of a gene in a population.
sex-linked gene
Sex-linked gene: Gene located on the sex chromosomes, exhibiting different inheritance patterns between males and females.
pseudoautosomal region (PAR)
Pseudoautosomal regions (PARs) are specific regions of the X and Y chromosomes that share homologous sequences and undergo recombination during meiosis. These regions are termed “pseudoautosomal” because they behave like autosomes in terms of recombination, despite being located on sex chromosomes. PARs are essential for the proper pairing and segregation of the X and Y chromosomes during meiosis, ensuring accurate transmission of genetic information. Recombination in PARs allows for the exchange of genetic material between the X and Y chromosomes, contributing to genetic diversity.
pleiotropy
Pleiotropy refers to a genetic phenomenon where a single gene influences multiple, seemingly unrelated traits or phenotypes. In other words, a mutation in a single gene can have effects on multiple aspects of an organism’s phenotype. This can occur because genes often play roles in multiple biochemical pathways or have diverse functions within cells or organisms. Pleiotropy is an important concept in genetics and can have significant implications for understanding the genetic basis of complex traits and diseases.
Be able to connect protein function to incomplete or codominance
In incomplete dominance and co-dominance:
- Incomplete: Heterozygotes show partial protein function, leading to an intermediate phenotype.
- Co-dominance: Both alleles produce functional proteins with distinct properties, resulting in simultaneous expression of both phenotypes.
Be able to identify dominance rules for a gene with multiple allelism and the interaction between two alleles for a gene with multiple allelism
In multiple allelism:
- Complete dominance: One allele fully masks others.
- Incomplete dominance: Alleles blend in heterozygotes.
- Co-dominance: Multiple alleles are equally dominant, fully expressed.
Determine if a gene is sex-linked based on relevant information (like ratios according to
sex)
- Sex-linked genes are located on the sex chromosomes, X and Y.
- In humans, females have two X chromosomes (XX), while males have one X and one Y chromosome (XY).
- To determine if a gene is sex-linked, examine the inheritance pattern in offspring. Look for differences in ratios between males and females.
- If a gene is located on the X chromosome and shows a different inheritance pattern in males and females, it is likely sex-linked.
- Inheritance patterns of sex-linked genes often result in different ratios between males and females in a population.
- For example, in X-linked recessive traits, males are more commonly affected because they have only one X chromosome. Females need two copies of the recessive allele to express the trait.
- Conversely, X-linked dominant traits may affect both males and females, but males often show more severe symptoms since they only have one X chromosome.
- Y-linked traits are passed from fathers to sons and are typically rare because the Y chromosome is much smaller and carries fewer genes compared to the X chromosome.
- Analyzing pedigree charts and observing the pattern of inheritance across generations can also help determine if a gene is sex-linked.
- Genetic testing and molecular techniques can provide definitive evidence of whether a gene is sex-linked by identifying its location on the sex chromosomes.
Understand how to use independent assortment to produce gametes when considering 2 genes on different chromosomes
- Independent assortment is a principle of genetics stating that alleles of different genes segregate independently during the formation of gametes.
- When considering two genes located on different chromosomes, their alleles assort independently of each other during gamete formation.
- This means that the inheritance of one gene does not influence the inheritance of the other gene.
- During meiosis, homologous chromosomes segregate independently into daughter cells, resulting in a random assortment of alleles from different genes into gametes.
- The number of possible gamete combinations is determined by the number of chromosome pairs undergoing independent assortment.
- For example, if an individual is heterozygous (AaBb) for two genes located on different chromosomes, independent assortment results in four different gamete combinations: AB, Ab, aB, and ab.
- The principle of independent assortment contributes to genetic variation within populations by generating diverse combinations of alleles in gametes.
- This process allows for the creation of unique genotypes in offspring, enhancing genetic diversity and adaptability within a population.
Calculate frequencies of genotypes and phenotypes in offspring in crosses with >1 gene
- Identify the parental genotypes: Determine the genotypes of the parents for each gene involved in the cross.
- Determine the possible gametes: List all possible gametes that each parent can produce for each gene.
- Construct a Punnett square or use probability calculations: For each gene, create a Punnett square or use probability calculations to determine the genotypic and phenotypic ratios in the offspring.
- Combine results for multiple genes: If there are multiple genes involved, combine the results from each gene to determine the overall frequencies of genotypes and phenotypes in the offspring.
- Calculate frequencies: Count the number of each genotype and phenotype in the offspring and calculate their frequencies by dividing the count by the total number of offspring.
- Consider linkage and recombination: If the genes are on the same chromosome and are linked, consider the possibility of recombination events affecting the genotypic and phenotypic ratios.
- Interpret the results: Analyze the frequencies to determine the expected distribution of genotypes and phenotypes in the offspring population.
- Compare with observed data: Compare the calculated frequencies with observed data from experiments or real-world populations to validate the predictions.
Skills: Making gametes, Punnetts, “and/or” probability rules, forkline if you like
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Making Gametes:
- For each parent, determine all possible gametes they can produce based on their genotype.
- If the parent is heterozygous (Aa), they can produce two types of gametes, each carrying one allele (A or a).
- If the parent is homozygous (AA or aa), they produce only one type of gamete, carrying the same allele.
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Punnett Squares:
- Use Punnett squares to predict the genotypic outcomes of offspring from a cross.
- Place the possible gametes from one parent along the top of the square and the possible gametes from the other parent along the side.
- Fill in the squares with combinations of gametes to determine the genotypes of the offspring.
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Probability Rules:
- Apply probability rules to determine the likelihood of each genotype in the offspring.
- Use the “and” rule: Multiply the probabilities of independent events to find the probability of both events occurring.
- Use the “or” rule: Add the probabilities of mutually exclusive events to find the probability of either event occurring.
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Forkline Method:
- The forkline method is a visual representation of the gamete combinations and their probabilities.
- Draw lines representing the possible gametes from each parent and label them with the corresponding alleles.
- Use branches to show all possible combinations of gametes and calculate the probability of each genotype in the offspring.
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Combining Skills:
- Use a combination of making gametes, Punnett squares, probability rules, and the forkline method to calculate frequencies of genotypes and phenotypes in offspring.
- Consider the inheritance patterns of each gene and whether they are linked or independent to make accurate predictions.
By employing these skills together, you can effectively analyze and predict the outcomes of crosses involving multiple genes and calculate the frequencies of genotypes and phenotypes in the offspring.
Understand linked genes do not independently assort and the consequences
Linked Genes:
- Linked genes are located on the same chromosome.
- They don’t independently assort during meiosis.
Consequences:
- Linked genes violate Mendel’s law of independent assortment.
- Offspring often inherit linked genes together, deviating from expected genetic ratios.
- This phenomenon, known as genetic linkage, affects genetic diversity and inheritance patterns.
- Understanding linked genes is crucial for accurate predictions in genetics.
Understand recombinant gametes for linked genes form at <50%
Calculate how far apart 2 genes are in cM
To calculate the distance between two genes in centimorgans (cM):Perform a cross.Count the number of recombinant offspring.Divide the number of recombinant offspring by the total offspring and multiply by 100.For example, if 20 out of 200 offspring are recombinant, the distance is (20/200)×100=10(20/200) \times 100 = 10(20/200)×100=10 cM.
Understand genes on the same chromosome can behave as if independently assorting if
greater than or equal to 50cM apart
Be able to determine cis/trans arrangement of alleles in the heterozygous parent in a
test cross for linkage
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Understand Cis and Trans Arrangements:
- In a cis arrangement, alleles of two linked genes are on the same chromosome and stay together during meiosis and gamete formation.
- In a trans arrangement, alleles of two linked genes are on different chromosomes or are far apart on the same chromosome and can segregate independently during meiosis.
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Perform a Test Cross:
- Cross the heterozygous individual (AaBb) with a homozygous recessive individual (aabb).
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Analyze the Offspring:
- Examine the phenotypes of the offspring resulting from the test cross.
- If the alleles of the two genes are in cis arrangement in the heterozygous parent, the gametes produced will carry either the dominant alleles (AB) or the recessive alleles (ab).
- If the alleles are in trans arrangement, the gametes produced will be Ab and aB.
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Observe the Progeny Ratios:
- If the linked genes are in cis arrangement in the heterozygous parent, the offspring will exhibit non-parental phenotypes at a low frequency.
- If the linked genes are in trans arrangement, the offspring will exhibit non-parental phenotypes at a higher frequency.
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Interpret the Results:
- A higher frequency of non-parental phenotypes suggests a trans arrangement, while a lower frequency suggests a cis arrangement.
- The ratio of parental to non-parental phenotypes can provide insight into the linkage arrangement of the alleles.
Determine the relative position of genes on chromosomes based on the frequency of
genetic recombination
The relative position of genes on chromosomes is determined by the frequency of genetic recombination. Genes that are closer together on a chromosome tend to have lower rates of recombination, while genes further apart exhibit higher rates. This principle, known as genetic linkage, allows researchers to estimate gene distances based on recombination frequencies, providing insights into chromosome structure and inheritance patterns.
linked gene
A linked gene refers to genes located on the same chromosome, often inherited together due to their physical proximity and tendency to be passed on as a unit during meiosis.
linkage
Linkage refers to the tendency of genes located close together on the same chromosome to be inherited together as a unit, rather than independently assorting during meiosis.
centimorgan (cM)
A centimorgan (cM) is a unit of measure used to quantify the relative distance between genes on a chromosome based on the frequency of genetic recombination between them during meiosis. It represents a 1% chance of recombination occurring between two loci on average.
map unit
A map unit, also known as a centimorgan (cM), is a measurement unit used in genetics to quantify the distance between two genes on a chromosome. One map unit is equivalent to a 1% chance of genetic recombination occurring between two loci during meiosis.
recombinant/recombination frequency
Recombinant frequency, also known as recombination frequency, refers to the proportion of offspring that display new combinations of alleles compared to the parental generation during genetic recombination. It is typically expressed as a percentage or a fraction and is used to estimate the distance between genes on a chromosome.
Be able to calculate probabilities with mixed rules (ex: complete dominance in one gene and incomplete dominance in a different gene)
Here are the key steps to calculate probabilities with mixed rules (e.g. complete dominance for one gene and incomplete dominance for another gene):
1) Assign genotypic symbols for each gene/trait
- For complete dominance: Capital letter (A) = dominant, lowercase (a) = recessive
- For incomplete dominance: Capital letters represent different alleles (C, c)
2) Determine parental genotypes and gamete formation
- Complete dominance: Aa will form A and a gametes
- Incomplete dominance: Cc will form C and c gametes
3) Set up a Punnett square combining all possible gamete combinations
4) Fill in genotypes in the Punnett square boxes based on the assigned symbols
5) Identify the phenotypic ratios for each trait based on dominance relationships
- Complete: 3:1 ratio if one parent is heterozygous
- Incomplete: 1:2:1 ratio if parents are heterozygous
6) Calculate probability by counting genotype numbers and dividing by total
This allows you to predict genotypic and phenotypic ratios when working with mixed dominance rules for different genes in a single cross.
Be able to set up a test cross for linkage and/or look at a test cross result and decide if
the genes are linked, calculate distance in cM, and also be able to tell if the alleles for
the linked genes are in cis or trans
Here are the key steps to set up a test cross for linkage, analyze the results, calculate map distance in centiMorgans (cM), and determine if linked alleles are in cis or trans configuration:
Setting up a test cross:
- Cross an individual with unknown genotype (doubly heterozygous) to a homozygous recessive individual
- Example: AaBb x aabb
Analyzing results:
- If genes are unlinked (on different chromosomes), you’ll see 1:1:1:1 ratio of parental types:non-parental types
- If genes are linked, the parental types will be more frequent than non-parental types
Calculating map distance:
- Map distance in cM = (# recombinant offspring / total offspring) x 100
- More recombinants = greater distance between genes on chromosome
Determining cis vs trans:
- Cis = Linked alleles on the same chromosome
- Trans = Linked alleles on different homologous chromosomes
- If parental genotypes are more frequent than recombinants, alleles are in cis
- If recombinant genotypes are more frequent, alleles are in trans
So by setting up a testcross, you can detect linkage, quantify it by map distance, and discern whether linked alleles started on the same or different homologous chromosomes.
Understand some traits are controlled by multiple genes – call them multigene traits
understand difference between 1 gene = 1 trait, 1 gene = >1 trait (pleiotropy), 2 gene =
2 trait (same as 1 gene =1 trait), vs. 2+ gene = 1 trait (multigene trait)
Got it, here’s an overview of the different gene-to-trait relationships:
1 gene = 1 trait
- Classic Mendelian inheritance pattern
- One gene controls one phenotypic trait
- Example: Pea plant height controlled by one gene (TT or Tt = tall, tt = short)
1 gene = >1 trait (pleiotropy)
- One gene influences multiple phenotypic traits
- Example: Sickle-cell anemia gene affects red blood cell shape and ability to carry oxygen
2 genes = 2 traits (same as 1 gene = 1 trait)
- Each gene controls a different single trait
- Traits assorted independently in inheritance
2+ genes = 1 trait (multigene or polygenic traits)
- Multiple genes contribute to and influence a single phenotypic trait
- Genes have additive effects or interact in complex ways
- Example: Human height, skin color influenced by many genes
Key Differences:
- Multigene traits controlled by several genes, not a single gene
- Effects are additive or showing complex interactions
- Don’t follow simple Mendelian inheritance patterns
Understanding these distinctions is important for interpreting trait inheritance patterns beyond just single gene traits.
Describe a quantitative trait (one type of one trait being controlled by multiple genes)
Know the difference between a discrete and continuous trait.
No punnetts or probability involved - just be able to tell given description of
scenario if it is describing a quantitative trait (like the question on the do you
understand)
A quantitative trait is a characteristic influenced by multiple genes, resulting in a wide range of phenotypic variations. It could be something like height or weight in humans. Discrete traits have distinct categories, like eye color (blue, brown, green), while continuous traits exist on a spectrum, like height or weight. So, if the trait can vary across a spectrum rather than falling into distinct categories, it’s likely a quantitative trait.
Describe recessive epistasis (subtype of multigene; also called gene interaction)
Recessive epistasis occurs when the presence of one gene masks the expression of another gene at a different locus. In this case, the allele of one gene (the epistatic gene) completely suppresses the expression of alleles of another gene (the hypostatic gene). This often results in a 9:3:4 phenotypic ratio in the offspring when two genes are involved in a dihybrid cross. An example would be the coat color in Labrador retrievers, where the presence of a specific allele in one gene masks the expression of alleles in another gene controlling coat color.
Describe dominant epistasis(subtype of multigene; also called gene interaction)
Dominant epistasis occurs when the presence of one allele of a gene masks the expression of alleles at a different locus, regardless of whether the allele is dominant or recessive. In other words, the dominant allele of one gene suppresses the expression of alleles of another gene. An example is the coat color in squash plants, where the presence of a dominant allele at one gene locus masks the expression of alleles at another gene locus controlling pigment production.
Describe complementary gene action(subtype of multigene; also called gene
interaction)
Complementary gene action occurs when two different genes work together to produce a specific phenotype. In this interaction, both genes need to contribute a functional allele for the trait to be expressed. However, the presence of either gene alone is not sufficient to produce the phenotype. An example is the flower color in sweet peas, where one gene controls the production of pigment and another gene controls the production of an enzyme required for pigment synthesis. Only when both functional alleles are present can the flower exhibit the desired color.
Explain how environmental effects influence phenotypes
o Understand how the environment can affect protein production (central dogma)
or protein function/activity to impact phenotypes though genotypes are the
same
o No probability problems. Just scenario given and you tell me it must be an
environmental effect (like the question on the do you understand).
Environmental effects can influence phenotypes in several ways. For example, environmental factors can affect the expression of genes involved in protein production, leading to differences in protein abundance or activity. Additionally, environmental conditions such as temperature, pH, and nutrient availability can directly impact protein folding and function. Even if individuals have the same genotype, differences in their environments can lead to variations in phenotype due to these environmental influences on gene expression and protein function.
multi-genic trait (big umbrella term for 2 genes = 1 trait)
A multi-genic trait, also known as a polygenic trait, refers to a characteristic that is controlled by the combined action of multiple genes. These genes often interact in complex ways to produce the phenotype. Traits such as height, weight, skin color, and intelligence are examples of polygenic traits in humans. Unlike traits controlled by a single gene (monogenic traits), polygenic traits exhibit a continuous range of variation rather than distinct categories.
epistasis
Epistasis is a genetic phenomenon where the expression of one gene masks or modifies the expression of another gene at a different locus. This interaction can result in unexpected phenotypic ratios in offspring. There are different types of epistasis, including dominant and recessive epistasis, where one gene suppresses the expression of another gene’s alleles. Epistasis plays a significant role in shaping the inheritance patterns of traits in various organisms.
Understand how multigene traits might present themselves phenotypically and
genotypically
Multigene traits can present themselves phenotypically in a variety of ways due to the complex interactions between multiple genes. Phenotypes of multigene traits often exhibit continuous variation, meaning they fall along a spectrum rather than distinct categories. This results in a wide range of phenotypic expressions within a population. For example, in the case of human height, multiple genes contribute to the overall height of an individual, leading to a continuous distribution of heights ranging from short to tall. Similarly, traits such as skin color, intelligence, and susceptibility to diseases are influenced by the combined effects of multiple genes and environmental factors, resulting in a spectrum of phenotypic variations.
Be able to deduce if epistasis is occurring. Need to know the genotype and phenotype
ratios of dihybrid for epistasis:
a. Recessive epistasis - 9:3:4
b. Dominant epistasis – 12:3:1
c. Complementary genes – 9:7
Be able to identify the dominant and recessive alleles in the non-epistatic gene
In the context of identifying dominant and recessive alleles in a non-epistatic gene, it’s important to recognize that the non-epistatic gene is the gene whose expression is affected by the epistatic gene.
Let’s consider a hypothetical scenario where Gene A is the epistatic gene and Gene B is the non-epistatic gene. If Gene A is dominant, it will mask the expression of Gene B. In this case, the dominant allele of Gene A will prevent the expression of the alleles of Gene B. Therefore, the alleles of Gene B that are unaffected by the dominant allele of Gene A will be expressed, and those are the alleles we can identify as dominant or recessive based on their interaction.
For example:
- If the dominant allele of Gene A is present (AA or Aa), then regardless of the alleles of Gene B, the phenotype controlled by Gene B will not be expressed.
- If the recessive allele of Gene A is present (aa), then the phenotype controlled by Gene B will be expressed based on its own dominant and recessive alleles.
So, in this scenario, we can identify the dominant and recessive alleles of Gene B based on their expression when Gene A is recessive.
Be able to identify the epistatic gene
Identifying the epistatic gene involves recognizing which gene’s alleles have the overriding influence on the expression of another gene’s alleles. In other words, it’s the gene whose alleles mask or modify the expression of alleles of another gene at a different locus.
To identify the epistatic gene:
1. Look for the gene whose alleles suppress or modify the expression of alleles of another gene.
2. Determine if the presence of certain alleles of this gene alters the expected phenotypic ratio based on Mendelian inheritance patterns.
3. In a genetic cross, observe which gene’s alleles dominate in determining the phenotype of the offspring, even when alleles of another gene are present.
Once you’ve identified the gene whose alleles exert this overriding influence, you’ve found the epistatic gene in the genetic interaction.
Understand how to determine the mode of inheritance using a pedigree: autosomal
dom, autosomal recessive, X-link dom, X-link recessive
Determining the mode of inheritance using a pedigree involves analyzing patterns of inheritance within a family tree. Here’s how you can identify different modes of inheritance:
-
Autosomal Dominant Inheritance:
- In an autosomal dominant pedigree, affected individuals typically have an affected parent.
- The trait usually appears in every generation.
- Affected individuals have at least one affected parent.
- Both males and females are affected with equal frequency.
- If one parent is affected (heterozygous), there is a 50% chance of passing the trait to each child.
- A vertical pattern of inheritance is observed.
-
Autosomal Recessive Inheritance:
- In an autosomal recessive pedigree, affected individuals may have unaffected parents.
- The trait may skip generations.
- Affected individuals often have unaffected parents who are carriers.
- Males and females are equally affected.
- If both parents are carriers, there is a 25% chance of having an affected child.
- Consanguineous (related) matings increase the likelihood of autosomal recessive inheritance.
-
X-linked Dominant Inheritance:
- In an X-linked dominant pedigree, affected males pass the trait to all their daughters but not to their sons.
- Affected females pass the trait to both sons and daughters.
- Every affected individual has an affected parent.
- There is no male-to-male transmission.
- Affected males typically have unaffected fathers and affected mothers (if the mother is affected, all daughters will also be affected).
-
X-linked Recessive Inheritance:
- In an X-linked recessive pedigree, affected males usually have unaffected parents.
- The trait skips generations.
- Affected males are usually born to unaffected carrier mothers.
- Affected females are usually born to carrier mothers and affected fathers.
- All daughters of affected fathers are carriers, but no sons are affected.
- Males are more frequently affected than females.
By examining these patterns within a pedigree, you can determine the mode of inheritance for a particular trait.
Make sure you know and stick to the order of questions to ask yourself when solving
pedigrees.
a. Always dominant or recessive first
b. Then ask is it X-linked
Remember you are looking for the MOST LIKELY inheritance mode. NOT any possibility.
Understand the sheer scale and size of the human genome – 3 billion bases.
Understand most of the human genome is non-coding 98.5% while only 1.5% is coding
(gene sequences)
Describe Genome-Wide Association Studies
GWAS, or Genome-Wide Association Studies, are research methods used to find genetic variations linked with specific traits or diseases across an entire genome. Researchers collect DNA samples from many individuals, both affected and unaffected, then compare the genetic differences between them to identify associations with the trait or disease being studied. By analyzing millions of genetic markers, researchers can pinpoint regions of the genome associated with the trait or disease. GWAS have been crucial in understanding the genetic basis of various conditions and traits, from diabetes to height.
Apply linkage to understand how genome wide association studies can be used to
identify genes associated with phenotypes
o Understand why a SNP associates with a phenotype because of linkage
o Understand that crossing over breaks apart associations for far apart SNPs and
phenotypes
In GWAS, linkage refers to the tendency of nearby genetic markers (like SNPs) to be inherited together. SNPs close to genes affecting traits are more likely to be inherited with those genes. Crossing over during meiosis can break apart associations between distant SNPs and traits by shuffling genetic material.
Understand that an associated SNP is not necessarily a mutation within a gene but can
be in a non-coding region.
o The associating SNP is simply traveling with some nearby gene that causes the
phenotype just because it is linked.
genome
The genome refers to the complete set of genetic material (DNA) present in an organism. It includes all the genes, as well as non-coding sequences, within the chromosomes of an organism. The genome contains the instructions for the development, functioning, and reproduction of the organism. In humans, the genome consists of approximately 3 billion base pairs of DNA organized into 23 pairs of chromosomes.
GWAS
GWAS stands for Genome-Wide Association Studies. These studies analyze genetic variations across the entire genome to identify associations between specific genetic variants (such as SNPs) and traits or diseases. GWAS have been instrumental in understanding the genetic basis of complex traits and diseases, from height and weight to diabetes and cancer. They help researchers pinpoint regions of the genome that may influence particular traits or diseases, offering insights into potential biological mechanisms and targets for further investigation and treatment.
non-coding
Non-coding DNA refers to regions of the genome that do not contain instructions for producing proteins. While coding DNA contains genes that encode proteins, non-coding DNA does not directly produce proteins but still plays important roles in gene regulation, chromosome structure, and other cellular processes. Non-coding DNA includes regulatory sequences, such as promoters and enhancers, as well as structural elements like telomeres and centromeres. Despite not coding for proteins, non-coding DNA is crucial for the proper functioning and regulation of genes within the genome.
coding
Coding DNA, also known as exons, refers to the regions of the genome that contain the instructions for producing proteins. These sequences are transcribed into messenger RNA (mRNA) during the process of gene expression and are subsequently translated into amino acids, which then form proteins. Coding DNA is characterized by the presence of open reading frames (ORFs) that can be translated into functional protein sequences. Mutations in coding DNA can lead to changes in the amino acid sequence of proteins, potentially altering their structure and function, and contributing to genetic diseases or variations in traits.
The ploidy of a cell
is the number of
complete genomes in a cell. We represent
this with n, 2n, 3n, 4n, etc
Haploid number
is the number of
chromosomes in one genome
Diploid means
two complete genomes or
two complete sets of chromosomes
When we have more
than one complete
genome, we will have
homologs
Homologous chromosomes can have different alleles for any given gene.
They can also have the same alleles for a given gene.
Homologs are not identical
especially when you consider all
the genes! Same genes at
everyone position but may have
different alleles for each gene
Germ cells
cells in ovaries and testes that
create gametes
Gametes
sex cells (egg/sperm)
Somatic cells
cells in all other areas of
body (arise when zygote grows and
develops through mitotic division)
Germ cells need a special division process
to reduce ploidy to create haploid
gametes from diploid germ cell. MEIOSIS!
Meiosis I goal:
separate every homologous chromosome – we stick
homologs together, align, and separate them
Meiosis II goal
one duplicate (sister) in each cell – basically mitosis to
separate sisters in meiosis II
Interphase
Uncondensed
chromosomes replicate in
parent cell (2n germ cell)
Prophase I (early)
Nuclear envelope begins to break down
* Chromosomes condense
* The spindle apparatus begins to form
* The homolog pairs come together in a pairing process
called synapsis
* The structure that results from synapsis is called a
bivalent, consisting of two homologs
* The chromatids of the homologs are called non-sister
chromatids
Prophase I (late):
- Synaptonemal complex removed
- Homologs remain attached at chiasmata
- Exchange or crossing over between
homologous non-sister chromatids occurs - Produces chromosomes with a combination of
maternal and paternal alleles
