Phenotype is the set of observable characteristics or traits of an organism. The term covers the organism’s morphology or physical form and structure, its developmental processes, its biochemical and physiological properties, its behavior, and the products of behavior. An organism’s phenotype results from two basic factors: the expression of an organism’s genetic code, or its genotype, and the influence of environmental factors. Both factors may interact, further affecting phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented example of polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. Richard Dawkins in 1978[rx] and then again in his 1982 book The Extended Phenotype suggested that one can regard bird nests and other built structures such as caddis-fly larvae cases and beaver dams as “extended phenotypes”.
Phenotype
Any given gene will usually cause an observable change in an organism, known as the phenotype. The terms genotype and phenotype are distinct for at least two reasons:
- To distinguish the source of an observer’s knowledge (one can know about genotype by observing DNA; one can know about phenotype by observing outward appearance of an organism).
- Genotype and phenotype are not always directly correlated. Some genes only express a given phenotype in certain environmental conditions. Conversely, some phenotypes could be the result of multiple genotypes. The genotype is commonly mixed up with the phenotype which describes the end result of both the genetic and the environmental factors giving the observed expression (e.g. blue eyes, hair color, or various hereditary diseases).
A simple example to illustrate genotype as distinct from phenotype is the flower colour in pea plants (see Gregor Mendel). There are three available genotypes, PP (homozygous dominant ), Pp (heterozygous), and pp (homozygous recessive). All three have different genotypes but the first two have the same phenotype (purple) as distinct from the third (white).
A more technical example to illustrate genotype is the single-nucleotide polymorphism or SNP. A SNP occurs when corresponding sequences of DNA from different individuals differ at one DNA base, for example where the sequence AAGCCTA changes to AAGCTTA.[rx] This contains two alleles : C and T. SNPs typically have three genotypes, denoted generically AA Aa and aa. In the example above, the three genotypes would be CC, CT and TT. Other types of genetic marker, such as microsatellites, can have more than two alleles, and thus many different genotypes.
Penetrance is the proportion of individuals showing a specified genotype in their phenotype under a given set of environmental conditions.[rx]
The Process and Purpose of Gene Expression Regulation
Gene expression is a highly complex, regulated process that begins with DNA transcribed into RNA, which is then translated into protein.
Key Points
Every cell within an organism shares the same genome (with exceptions, i.e. mature red blood cells), but has variation between its proteomes.
Gene expression involves the process of transcribing DNA into RNA and then translating RNA into proteins.
Gene expression is a highly complex and tightly-regulated process.
Key Terms
- somatic: part of, or relating to the body of an organism
- genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
- proteome: the complete set of proteins encoded by a particular genome
Each somatic cell in the body generally contains the same DNA. A few exceptions include red blood cells, which contain no DNA in their mature state, and some immune system cells that rearrange their DNA while producing antibodies. In general, however, the genes that determine whether you have green eyes, brown hair, and how fast you metabolize food are the same in the cells in your eyes and your liver, even though these organs function quite differently. If each cell has the same DNA, how is it that cells or organs are different? Why do cells in the eye differ so dramatically from cells in the liver ?
Gene Expression: The genetic content of each somatic cell in an organism is the same, but not all genes are expressed in every cell. The control of which genes are expressed dictates whether a cell is (a) an eye cell or (b) a liver cell. It is the differential gene expression patterns that arise in different cells that give rise to (c) a complete organism.
Whereas each cell shares the same genome and DNA sequence, each cell does not turn on, or express, the same set of genes. Each cell type needs a different set of proteins to perform its function. Therefore, only a small subset of proteins is expressed in a cell that constitutes its proteome. For the proteins to be expressed, the DNA must be transcribed into RNA and the RNA must be translated into protein. In a given cell type, not all genes encoded in the DNA are transcribed into RNA or translated into protein because specific cells in our body have specific functions. Specialized proteins that make up the eye (iris, lens, and cornea) are only expressed in the eye, whereas the specialized proteins in the heart (pacemaker cells, heart muscle, and valves) are only expressed in the heart. At any given time, only a subset of all of the genes encoded by our DNA are expressed and translated into proteins. The expression of specific genes is a highly-regulated process with many levels and stages of control. This complexity ensures the proper expression in the proper cell at the proper time.
In this section, you will learn about the various methods of gene regulation and the mechanisms used to control gene expression, such as: epigenetic, transcriptional, post-transcriptional, translational, and post-translational controls in eukaryotic gene expression, and transcriptional control in prokaryotic gene expression.
The Relationship Between Genes and Proteins
Proteins, encoded by individual genes, orchestrate nearly every function of the cell.
Key Points
Genes are composed of DNA arranged on chromosomes.
Some genes encode structural or regulatory RNAs. Other genes encode proteins.
Replication copies DNA; transcription uses DNA to make complementary RNAs; translation uses mRNAs to make proteins.
In eukaryotic cells, replication and transcription take place within the nucleus while translation takes place in the cytoplasm.
In prokaryotic cells, replication, transcription, and translation occur in the cytoplasm.
Key Terms
- DNA: a biopolymer of deoxyribonucleic acids (a type of nucleic acid) that has four different chemical groups, called bases: adenine, guanine, cytosine, and thymine
- messenger RNA: Messenger RNA (mRNA) is a molecule of RNA that encodes a chemical “blueprint” for a protein product.
- protein: any of numerous large, complex naturally-produced molecules composed of one or more long chains of amino acids, in which the amino acid groups are held together by peptide bonds
Genes and Proteins
Since the rediscovery of Mendel’s work in 1900, the definition of the gene has progressed from an abstract unit of heredity to a tangible molecular entity capable of replication, transcription, translation, and mutation. Genes are composed of DNA and are linearly arranged on chromosomes. Some genes encode structural and regulatory RNAs. There is increasing evidence from research that profiles the transcriptome of cells (the complete set all RNA transcripts present in a cell) that these may be the largest classes of RNAs produced by eukaryotic cells, far outnumbering the protein-encoding messenger RNAs (mRNAs), but the 20,000 protein-encoding genes typically found in animal cells, and the 30,o00 protein-encoding genes typically found in plant cells, nonetheless have huge impacts on cellular functioning.
Protein-encoding genes specify the sequences of amino acids, which are the building blocks of proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell. Both protein-encoding genes and the proteins that are their gene products are absolutely essential to life as we know it.
Genes Encode Proteins: Genes, which are carried on (a) chromosomes, are linearly-organized instructions for making the RNA and protein molecules that are necessary for all of processes of life. The (b) interleukin-2 protein and (c) alpha-2u-globulin protein are just two examples of the array of different molecular structures that are encoded by genes.
Replication, Transcription, and Translation are the three main processes used by all cells to maintain their genetic information and to convert the genetic information encoded in DNA into gene products, which are either RNAs or proteins, depending on the gene. In eukaryotic cells, or those cells that have a nucleus, replication and transcription take place within the nucleus while translation takes place outside of the nucleus in cytoplasm. In prokaryotic cells, or those cells that do not have a nucleus, all three processes occur in the cytoplasm.
Replication is the basis for biological inheritance. It copies a cell’s DNA. The enzyme DNA polymerase copies a single parental double-stranded DNA molecule into two daughter double-stranded DNA molecules. Transcription makes RNA from DNA. The enzyme RNA polymerase creates an RNA molecule that is complementary to a gene-encoding stretch of DNA. Translation makes protein from mRNA. The ribosome generates a polypeptide chain of amino acids using mRNA as a template. The polypeptide chain folds up to become a protein.
Chromosomal Theory of Inheritance
The Chromosomal Theory of Inheritance identified chromosomes as the genetic material responsible for Mendelian inheritance.
Key Points
Homologous chromosome pairs are independent of other chromosome pairs.
Chromosomes from each homologous pair are sorted randomly into pre- gametes.
Parents synthesize gametes that contain only half of their chromosomes; eggs and sperm have the same number of chromosomes.
Gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents.
Eye color in fruit flies was the first X-linked trait to be discovered; thus, Morgan’s experiments with fruit flies solidified the Chromosomal Theory of Inheritance.
Key Terms
- autosome: any chromosome other than sex chromosomes
- hemizygous: having some single copies of genes in an otherwise diploid cell or organism
- wild type: the typical form of an organism, strain, gene or characteristic as it occurs in nature
Chromosomal Theory of Inheritance
The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and re-evaluate his model in terms of the behavior of chromosomes during mitosis and meiosis. In 1902, Theodor Boveri observed that proper embryonic development of sea urchins does not occur unless chromosomes are present. That same year, Walter Sutton observed the separation of chromosomes into daughter cells during meiosis. Together, these observations led to the development of the Chromosomal Theory of Inheritance, which identified chromosomes as the genetic material responsible for Mendelian inheritance.
The Chromosomal Theory of Inheritance was consistent with Mendel’s laws and was supported by the following observations:
- During meiosis, homologous chromosome pairs migrate as discrete structures that are independent of other chromosome pairs.
- The sorting of chromosomes from each homologous pair into pre-gametes appears to be random.
- Each parent synthesizes gametes that contain only half of their chromosomal complement.
- Even though male and female gametes (sperm and egg) differ in size and morphology, they have the same number of chromosomes, suggesting equal genetic contributions from each parent.
- The gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents.
Despite compelling correlations between the behavior of chromosomes during meiosis and Mendel’s abstract laws, the Chromosomal Theory of Inheritance was proposed long before there was any direct evidence that traits were carried on chromosomes. Critics pointed out that individuals had far more independently segregating traits than they had chromosomes. It was only after several years of carrying out crosses with the fruit fly, Drosophila melanogaster, that Thomas Hunt Morgan provided experimental evidence to support the Chromosomal Theory of Inheritance.
In 1910, Thomas Hunt Morgan started his work with Drosophila melanogaster, a fruit fly. He chose fruit flies because they can be cultured easily, are present in large numbers, have a short generation time, and have only four pair of chromosomes that can be easily identified under the microscope. They have three pair of autosomes and a pair of sex chromosomes. At that time, he already knew that X and Y have to do with gender. He used normal flies with red eyes and mutated flies with white eyes and cross bred them. In flies, the wild type eye color is red (XW) and is dominant to white eye color (Xw). He was able to conclude that the gene for eye color was on the X chromosome. This trait was thus determined to be X-linked and was the first X-linked trait to be identified. Males are said to be hemizygous, in that they have only one allele for any X-linked characteristic.
Eye Color in Fruit Flies: In Drosophila, the gene for eye color is located on the X chromosome. Red eye color is wild type and is dominant to white eye color.
References
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