2.7 Unit Summary and Review

The Genome

Eukaryotes have multiple, linear chromosomes surrounded by a nuclear membrane. Human somatic cells have 46 chromosomes consisting of two sets of 22 homologous chromosomes and a pair of nonhomologous sex chromosomes. This is the 2n, or diploid, state. Human gametes have 23 chromosomes or one complete set of chromosomes. This is the n, or haploid, state. Genes are segments of DNA that code for a specific protein or RNA molecule. An individual’s traits are the observable or measurable features of an organism which are determined in large part by the genes inherited from each parent, but also by the environment that they experience. An individual’s phenotype encompasses all traits, including those that are visible and those that are not (such as behavior). Genes are expressed as characteristics of the organism, and each characteristic may have different variants called traits that are caused by differences in the DNA sequence for a gene, which can be the distinguishing feature between two individuals.

The Cell Cycle

The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase. Interphase is divided into G1, S, and G2 phases. Mitosis consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase. Mitosis is usually accompanied by cytokinesis, during which the cytoplasmic components of the daughter cells are separated by an actin ring (animal cells). Each step of the cell cycle is monitored by internal controls called checkpoints. There are three major checkpoints in the cell cycle: one near the end of G1, a second at the G2–M transition, and the third during metaphase.

Cancer and the Cell Cycle

Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms regulating the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to the daughter cells. Each successive cell division will give rise to daughter cells with even more accumulated damage. Eventually, all checkpoints become nonfunctional, and rapidly reproducing cells crowd out normal cells, resulting in tumorous growth.

The Cellular Basis of Inheritance

Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be one of the advantages of sexual reproduction that has made it so successful. Meiosis and fertilization alternate in sexual life cycles. The process of meiosis produces genetically unique reproductive cells called gametes, which have half the number of chromosomes as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced and the timing between meiosis and fertilization vary greatly. There are three main categories of life cycles: diploid-dominant, demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and alternation of generations, demonstrated by plants and some algae.

Meiosis

Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid offspring. The process that results in haploid cells is called meiosis. Meiosis is a series of events that arrange and separate chromosomes into daughter cells. During the interphase of meiosis, each chromosome is duplicated. In meiosis, there are two rounds of nuclear division resulting in four nuclei and usually four haploid daughter cells, each with half the number of chromosomes as the parent cell. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I and random alignment at metaphase I. The cells that are produced by meiosis are genetically unique.

Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions are two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set rather than the two sets the parent cell had. The main differences between the processes occur in the first division of meiosis. The homologous chromosomes separate into different nuclei during meiosis I causing a reduction of ploidy level. The second division of meiosis is much more similar to a mitotic division.

Patterns of Inheritance

Working with garden pea plants, Mendel found that crosses between parents that differed for one trait produced F1 offspring that all expressed one parent’s traits. The traits that were visible in the F1 generation are referred to as dominant, and traits that disappear in the F1 generation are described as recessive. When the F1 plants in Mendel’s experiment were self-crossed, the F2 offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully from the original P parent. Reciprocal crosses generated identical F1 and F2 offspring ratios. By examining sample sizes, Mendel showed that traits were inherited as independent events.

When true-breeding, or homozygous, individuals that differ for a certain trait are crossed, all of the offspring will be heterozygous for that trait. If the traits are inherited as dominant and recessive, the F1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F2 offspring will exhibit a ratio of three dominant to one recessive.

Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a diploid individual. In addition, genes are assorted into gametes independently of one another. That is, in general, alleles are not more likely to segregate into a gamete with a particular allele of another gene.

Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles for a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two.

According to Mendel’s law of independent assortment, genes sort independently of each other into gametes during meiosis. This occurs because chromosomes, on which the genes reside, assort independently during meiosis and crossovers cause most genes on the same chromosomes to also behave independently. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together. This results in offspring ratios that violate Mendel’s law of independent assortment. However, recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together. Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal space.

Whether or not they are sorting independently, genes may interact at the level of gene products, such that the expression of an allele for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis.

DNA Structure and Function

The model of the double-helix structure of DNA was proposed by Watson and Crick. The DNA molecule is a polymer of nucleotides. Each nucleotide is composed of a nitrogenous base, a five-carbon sugar (deoxyribose), and a phosphate group. There are four nitrogenous bases in DNA, two purines (adenine and guanine) and two pyrimidines (cytosine and thymine). A DNA molecule is composed of two strands. Each strand is composed of nucleotides bonded together covalently between the phosphate group of one and the deoxyribose sugar of the next. From this backbone extend the bases. The bases of one strand bond to the bases of the second strand with hydrogen bonds. Adenine always bonds with thymine, and cytosine always bonds with guanine. The bonding causes the two strands to spiral around each other in a shape called a double helix. Ribonucleic acid (RNA) is a second nucleic acid found in cells. RNA is a single-stranded polymer of nucleotides. It also differs from DNA in that it contains the sugar ribose, rather than deoxyribose, and the nucleotide uracil rather than thymine. Various RNA molecules function in the process of forming proteins from the genetic code in DNA.

Prokaryotes contain a single, double-stranded circular chromosome. Eukaryotes contain double-stranded linear DNA molecules packaged into chromosomes. The DNA helix is wrapped around proteins to form nucleosomes. The protein coils are further coiled, and during mitosis and meiosis, the chromosomes become even more greatly coiled to facilitate their movement. Chromosomes have two distinct regions which can be distinguished by staining, reflecting different degrees of packaging and determined by whether the DNA in a region is being expressed (euchromatin) or not (heterochromatin).

DNA replicates by a semi-conservative method in which each of the two parental DNA strands act as a template for new DNA to be synthesized. After replication, each DNA has one parental or “old” strand, and one daughter or “new” strand.

Replication in eukaryotes starts at multiple origins of replication, while replication in prokaryotes starts from a single origin of replication. The DNA is opened with enzymes, resulting in the formation of the replication fork. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides in only one direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase.

The ends of eukaryotic chromosomes pose a problem, as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected. Cells have mechanisms for repairing DNA when it becomes damaged or errors are made in replication. These mechanisms include mismatch repair to replace nucleotides that are paired with a non-complementary base and nucleotide excision repair, which removes bases that are damaged such as thymine dimers.

In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template. Elongation synthesizes new mRNA. Termination liberates the mRNA and occurs by mechanisms that stall the RNA polymerase and cause it to fall off the DNA template. Newly transcribed eukaryotic mRNAs are modified with a cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Eukaryotic mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs are exported from the nucleus to the cytoplasm.

The central dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is the correspondence between the three-nucleotide mRNA codon and an amino acid. The genetic code is “translated” by the tRNA molecules, which associate a specific codon with a specific amino acid. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three stop codons. This means that more than one codon corresponds to an amino acid. Almost every species on the planet uses the same genetic code.

The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit binds to the mRNA template. Translation begins at the initiating AUG on the mRNA. The formation of bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. The ribosome accepts charged tRNAs, and as it steps along the mRNA, it catalyzes bonding between the new amino acid and the end of the growing polypeptide. The entire mRNA is translated in three-nucleotide “steps” of the ribosome. When a stop codon is encountered, a release factor binds and dissociates the components and frees the new protein.

While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is regulated only at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels.