BIO101 Study Guide

9a. Explain how information flows from genotype to phenotype at the molecular level

• What is a genotype?
• What is a phenotype?
• How are genotype and phenotype different?
• What is the connection between genotype and phenotype?

We often say our genes give us our traits. This is true, but only indirectly. Genes are sequences of DNA, and these genes provide instructions for how to make corresponding sequences of RNA. These sequences of RNA, in turn, serve as instructions for how to build proteins.

Proteins are the final product of gene expression. The particular proteins that are built in the cells of an organism are what give that organism its traits. The proteins directly determine the traits, but the genes indirectly determine the traits, because the genes indirectly instruct the cells how to build the proteins.

There may be multiple possible traits for any given characteristic, such as black, brown, or red hair color. We call the trait an individual exhibits for a given characteristic, such as the black hair trait for the hair-color characteristic, that individual's phenotype. That phenotype depends on the proteins produced, which depends on the version of the corresponding gene (DNA) that individual possesses.

An individual's genotype refers to the DNA sequence for a particular gene. Consequently, your genotype indirectly determines your phenotype.

Review how these terms relate, and how they differ, in the section Phenotypes and Genotypes.

9b. Explain how the terms: genotype, phenotype, homozygous, heterozygous, dominant, recessive, co-dominant, and sex-linkage are used

• Distinguish between genotype and phenotype.
• Distinguish between homozygous and heterozygous.
• Distinguish between dominance and recessivity.
• What is co-dominance?
• What is sex linkage?

When scientists study organisms genetically, they usually focus on one single gene. A gene is a stretch of DNA coding for a particular protein – a gene controls a particular characteristic. Alternative versions of a gene (with different nucleotide sequences) are called alleles. A diploid cell features two alleles for any particular gene because a diploid cell features two of every kind of chromosome, one from each parent.

An individual's genotype is the sequence of symbols that represent the particular alleles an individual possesses for the gene being studied. Since alleles code for proteins, and proteins give organisms their traits, alleles indirectly determine phenotype. A phenotype is the observable trait an individual exhibits for the characteristic being studied. Since a diploid cell contains two alleles for a gene, there are two possibilities:

• Both alleles for the gene under study are the same version (they are identical). In this case, the individual is homozygous.

• The two alleles for the gene under study are different versions. In this case, the individual is heterozygous.

One allele is typically dominant over another allele, which is called recessive. When one or two dominant alleles occur in a cell, the dominant phenotype shows itself. For example, if there is just one dominant allele and the other allele is recessive, the single dominant allele will dominate over the recessive allele. The dominant phenotype is expressed (shows itself), but the recessive phenotype is not expressed. The only way a recessive phenotype is expressed is when both of the alleles are recessive. This individual is homozygous recessive.

A heterozygous individual features one dominant allele and one recessive allele and expresses the dominant phenotype. A homozygous dominant individual (both alleles are dominant) also expresses the dominant phenotype. Codominance describes a special case when two different alleles are both simultaneously expressed. In other words, one allele does not dominate the other. A good example is Type AB blood, which expresses both Type A and Type B phenotypes.

Sex linkage refers to a gene that is part of a sex chromosome. Consequently, the expression is different in males compared to females. For example, in humans, females have two X chromosomes, so they have two alleles for sex-linked genes. Males, on the other hand, have one X chromosome and one Y chromosome, but the Y chromosome does not have all of the genes that an X chromosome has. Therefore a male has only one allele for a sex-linked gene.

Make sure you understand these important definitions for the laws of inheritance before you proceed. Review Extensions of the Laws of Inheritance.

9c. Given a pedigree, infer whether the trait in the diagram is dominant or recessive, and indicate individual genotypes when possible

• What is a pedigree?
• How does a pedigree use symbols to indicate phenotypes?

A pedigree is merely a symbolic representation (or chart) of the phenotypes and sexes of individuals, with the ancestral relationships between these individuals. Keep the laws of inheritance in mind, as you study a pedigree to determine whether a given trait is dominant or recessive.

Once you determine the dominance/recessivity relationship, a pedigree is a useful tool for determining the possible genotypes of individuals, based on the phenotypes indicated in the chart.

For example, in this pedigree, the original parents (square and circle at the top) both carry the unaffected phenotype (because their symbols are not filled). They produced some offspring that were unaffected and some that were affected. The only way for this to be possible is if the affected phenotype is the recessive trait. An offspring with the affected (recessive) phenotype must be homozygous recessive; otherwise, that individual would have the unaffected (dominant) trait.

Therefore, each original parent must be heterozygous, because each parent must pass on a recessive allele to produce a homozygous recessive offspring. We can make the same inference about the two parents listed rightmost in the generation enclosed by the red dashes because they also produced recessive offspring. A good example of this is when two parents with black hair (dominant) have a child who has red hair (recessive).

Review Pedigrees for more on the laws of inheritance.

9d. Solve genetic problems involving monohybrid crosses with dominant and recessive traits, codominant traits, and sex-linked traits

• What is a genetic cross?
• How do you use a Punnett square?

A genetic cross is an incidence of sexual reproduction that involves a male and female from a particular species. A monohybrid cross is a cross where you are studying only one gene (one characteristic), and the two parents usually differ in their genotypes. For example, one parent might be homozygous dominant (AA) and the other might be homozygous recessive (aa).

Knowing the genotypes of the parents allows us to draw a Punnett square to represent the possible fertilization events involving these two parents. Fertilization is the fusion of a male gamete and a female gamete to produce a zygote.

A Punnett square lists (on adjacent sides of the square) all possible gametes that can be produced by each parent. By matching up each possible gamete from one parent with each possible gamete from the other parent, the boxes within a Punnett square list all possible zygotes that can be produced by these parents. Moreover, the ratio of different possible genotypes (the genotypic ratio) and of different corresponding phenotypes (the phenotypic ratio) can be computed for the generation created by the particular cross.

Review crosses in Introduction to Heredity. Practice constructing Punnett squares to make sure you understand the concepts they represent.

9e. Solve genetic problems involving dihybrid crosses with dominant and recessive traits, codominant traits, and sex-linked traits

• How is a dihybrid cross different from a monohybrid cross?
• How are they similar?

Once you know the genotypes (for a particular characteristic or gene) for two parents, it is possible to compute the probabilities of various genotypes or phenotypes in the offspring they produce. This is because the genotype of an offspring results from randomly selecting one of the two alleles for the gene in one parent, and randomly selecting one of the two alleles in the other parent.

The sperm and egg carry these randomly selected alleles. When the sperm and egg fuse (fertilization) to produce the zygote of the offspring, the genotype of the offspring is a combination of an allele from the father and an allele from the mother. For example, when a male with genotype Aa mates with a female with genotype $aa$, we symbolize this mating (or cross) as $Aa \times aa$.

The probability of an offspring having the $AA$ genotype

Having the $AA$ genotype requires receiving an $A$ allele from the father and an $A$ allele from the mother. The mother in this example has no $A$ allele, so the probability is zero.

The probability of an offspring having the $Aa$ genotype

Having this genotype requires receiving an $A$ allele from one parent (either one) and receiving an $a$ allele from the other parent. The probability of receiving an $A$ allele from the father is one-in-two (50% or 0.5). The probability of receiving an allele from the mother is two-in-two (100% or 1.0), because that is all she has to give. The overall probability for $Aa$ is the product of these two individual probabilities. 

In this case, it is 0.5 × 1.0 = 0.5. In other words, there is a 0.5 (50%) probability that any given offspring of these parents will have the $Aa$ genotype.

The probability of an offspring having the $aa$ genotype 

Using the same reasoning we used to compute $Aa$, there is also a 0.5 probability for the aa genotype, because there is a 0.5 probability of receiving an $a$ allele from the father, and a 1.0 probability of receiving an $a$ allele from the mother. The overall probability is 0.5 × 1.0 = 0.5.

In this example, aa is the only other possible genotype besides $Aa$.

You can think about fertilization as if you were to randomly choose a card from two cards a father holds, and then randomly choose a second card from two cards a mother holds. The two cards you draw (representing the sperm and egg) determine the two cards you (the offspring) will have (representing the genotype of the zygote). Keep this in mind as you review Mendel's Laws of Inheritance.

Like a monohybrid cross, a dihybrid cross is a genetic cross. This means it involves fertilization of a female gamete (from the female parent) by a male gamete (from the male parent) to produce zygotes that can develop into adult offspring. The fundamental difference between a monohybrid cross and a dihybrid cross is that a monohybrid cross tracks only gene (corresponding to one characteristic), whereas a dihybrid cross simultaneously tracks two different genes (corresponding to two different characteristics).

Since two different genes are studied, the genotypes in a dihybrid cross are longer sequences of symbols (both for the alleles and for the zygotes), because they need to indicate alleles for two genes. Also, because there are more possible combinations of alleles, a dihybrid cross will feature more boxes in its Punnett square compared to a monohybrid cross. These differences are illustrated in the generic examples shown below.

Monohybrid cross: $Aa$ (heterozygous male) $\times Aa$ (heterozygous female)

• Number of genes under study: One (Gene $A$)
• Genotypes of possible male gametes: $A$, $a$
• Genotypes of possible female gametes: $A$, $a$

• Punnett square:

Dihybrid cross: $AaBb$ (doubly heterozygous male) $\times AaBb$ (doubly heterozygous female)

• Number of genes under study: Two (Gene $A$ and Gene $B$)
• Possible male gametes: $AB$, $aB$, $Ab$, $ab$
• Possible female gametes: $AB$, $aB$, $Ab$, $ab$

• Punnett square:

Review the dihybrid example in the second video in Introduction to Heredity to ensure you understand how dihybrid crosses differ from monohybrid crosses.

9f. Define mutation and explain how mutations can result in an altered phenotype

• What is a mutation?
• How can mutation affect phenotype?

A mutation is an accidental change in the DNA sequence of an organism. An organism's DNA is arranged in chromosomes. Each chromosome is a long sequence of DNA nucleotides. A gene is a subsequence of DNA nucleotides within the longer sequence that makes up the chromosome. A mutation arises when the sequence gets changed – either by an error during DNA replication or by some other accident, such as exposure to certains chemicals or forms of radiation. The reason a gene is able to serve as a code (stored information) is due to its particular sequence of DNA nucleotides.

Mutation changes that sequence. The code is changed, and the RNA will also be altered when the altered code is used to make RNA. Similarly, when the code from the altered (mutated) version of RNA is used to build a protein, the protein may be different from the unmutated version.

Since proteins directly determine phenotypes, a mutant protein (resulting from a mutant form of DNA for the corresponding gene) may alter the phenotype. Mutation is the original source of genetic variation. It explains why we have different species and differences among individuals of the same species.

In the case of heterozygote advantage, heterozygous individuals are more fit than both types of homozygous individuals (homozygous dominant and homozygous recessive). For example, a mutant allele for a human hemoglobin gene codes for a mutant form of the hemoglobin protein. This situation is deleterious (causes harm or damage) because it causes sickle cell disease. However, the mutant form of hemoglobin also confers higher resistance to malaria.

A homozygous recessive individual will develop sickle-cell disease, which drastically reduces fitness. A homozygous dominant individual will not develop sickle-cell disease, but that person will not be resistant to malaria. However, a heterozygous individual will not develop sickle-cell disease (because the one normal allele will prevent the disorder), and they will also have increased resistance to malaria (because of the mutant allele).

Therefore, heterozygous individuals have the greatest chance of passing on their alleles to the next generation – this includes the mutant allele. The population maintains the sickle-cell allele by natural selection. To make sense of heterozygote advantage, review the laws of inheritance. Keep in mind that each allele is a code for a particular protein, and therefore each allele corresponds to a particular trait.

Review Mutations and Laws of Inheritance. As you continue to study genetics, keep in mind that accidental mutations are the source of differences in genotypes and phenotypes.

Unit 9 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• allele
• characteristic
• chromosome
• co-dominant
• cross
• dihybrid cross
• diploid
• DNA
• dominant
• egg
• fertilization
• fitness
• gamete
• gene
• genotype
• haploid
• heterozygote advantage
• heterozygous
• homozygous
• homozygous dominant
• homozygous recessive
• inheritance
• monohybrid cross
• mutant
• mutation
• natural selection
• nucleotide
• offspring
• parent
• pedigree
• phenotype
• probability
• protein
• Punnett square
• recessive
• RNA
• sex-linked
• sperm
• trait
• zygote