Chapter 4: DNA, Genes, and Protein Synthesis The cell is structurally and functionally the basic unit of life for all organisms. The term cell comes from Robert Hooke, who in the seventeenth century observed that cork was made up of small units, which reminded him of the "cells" or cubicles in which monks lived. All cells must arise from preexisting cells, and living organisms may be single-celled or multicellular in composition. Figure 4-1 A typical eukaryotic cell. Cells may be classified into two types depending on the presence of an internal, membranebound nucleus: (1) prokaryotic cells, which do not have a separate nucleus and are found in bacteria and cyanobacteria and (2) eukaryotic cells, which contain a true nucleus and make up all other forms of life. It is thought that the prokaryotic cells evolved first and that eukaryotic cells evolved from these simpler forms. All eukaryotic cells share certain struc- 62
tural features in common, including (1) a plasma membrane, separating the contents of the cell from the outside world; (2) cytoplasm, a gel-like or fluid-like matrix within the plasma membrane; (3) organelles, the various structures responsible for cell functions, such as metabolism and protein synthesis; and (4) genetic information, in the form of DNA (deoxyribonucleic acid), which is stored in the nucleus. Two types of cells are found in humans: (1) somatic cells and (2) gametes. The somatic cells are those cells that make up the body of an organism; everything from hair and skin to lungs, liver, muscles, blood, and bone. Somatic cells are often referred to as body cells. In contrast, the gametes, or sex cells, are the sperm found in the male testes and the ova (or egg cells) found in the female ovaries. The gametes carry the genetic information required to make the next generation. EXERCISE 1 Can you think of a reason why the gametes have only 23 chromosomes (one of each pair)? Chromosome Structure DNA and proteins are found on chromosomes. Chromosomes are located in the nucleus and are made up of long, threadlike material called chromatin that coils and condenses when a cell is about to divide, making the chromosome visible with a light microscope. Chromosomes are normally single stranded, but they become double stranded when DNA replicates itself, prior to cell division. Each strand is called a chromatid. When the chromosome is double stranded, the two chromatids are called sister chromatids. A constricted area, called the centromere, separates one chromatid strand into two "arms." Chromosomes come in different sizes and can be identified by size and position of their centromere. Centromeres may be in the middle of the chromosome, so that the arms are of approximately equal length, or they may be off center, making the arms of unequal length (Figure 4-2). Figure 4-2 Single-stranded and double-stranded chromosomes. 63
Different species have a different number of chromosomes in their cells. Normal human body cells contain 23 pairs of chromosomes (46 chromosomes total). The chromosomes are numbered 1 through 23. In other words, there are two copies of number 1, two copies of number 2, and so on, until you reach the two copies of number 23. These are called homologous pairs. The members of each pair are similar in size, position of the centromere, and genetic information carried (always for the same traits) (Figure 4-3). EXERCISE 2 Chimpanzees have 48 chromosomes in their somatic cells. How many chromosomes do you think are found in their sex cells? Genetic information is distributed along the length of the chromosome as genes: segments of DNA that code for specific traits. Alleles are alternate forms (versions) of a gene. For example, the gene for eye color may have several alleles, such as brown, blue, and green. The first 22 pairs of chromosomes are called the autosomes. Autosomes are always homologous pairs and contain information pertaining to body structure and function. The final, 23rd pair, are called the sex chromosomes. Human females have two X chromosomes as their 23rd pair (and are homologous), while human males have one X and one Y chromosome as their 23rd pair. Since the X and Y chromosome are different lengths they are not homologous. The Y chromosome carries information only pertaining to the biological sex of the individual. Human sex cells, or gametes, carry only one copy of each pair, so they have 23 chromosomes in each sperm or ovum. EXERCISE 3 Describe the difference between the autosomes and the sex chromosomes. When chromosomes are stained and photographed, the resulting image is called a karyotype (Figure 4-3). Chromosomes in a karyotype can be cut out and lined up. They may be arranged into pairs by matching their size and position of the centromere. The position of the centromere may be described as follows: Acrocentric -at one end, so arms are of unequal length Metacentric -in the middle, so that arms are of similar length Telocentric -all the way at one end, so that one arm is barely visible 64
Figure 4-3 A human karyotype. Notice the autosomes, sex chromosomes, and basic chromosome structure. EXERCISE 4 How do you determine the sex of an individual when examining his or her karyotype? What is the sex of the individual in figure 4-3? Sometimes, an individual is born with the wrong number of chromosomes. This is caused by a nondisjunction, a failure of the chromosomes to segregate properly during cell division. In this case, a person may have a different number of chromosomes in their karyotype due to a deletion or duplication of a chromosome. Some common abnormalities are: Turner Syndrome - X0, deletion of a sex chromosome. These are females who tend to be shorter than average, with below-average intelligence, and are infertile. Kleinfelter's Syndrome - XXY, an extra X chromosome. These males are taller than average, with below-average intelligence, and are infertile. XYY(Supermale) - an extra Y chromosome. These are males who may show a tendency toward aggressive behavior. Down syndrome - three copies of chromosome 21(trisomy 21). These individuals are characterized by a suite of traits, primarily mental retardation. EXERCISE 5 The following pages show the karyotypes of four individuals with a nondisjunction condition described above. On each karyotype: (1) write whether the person is male or female, (2) circle the abnormality, and (3) write the name of the condition. 65
a) b) 66
c) d) 67
Cell Division Cell division in eukaryotes requires two processes: division of the cytoplasm (cytokinesis) and division of the nucleus (mitosis or meiosis). Cytokinesis ensures that each end product (daughter cell) receives the cellular structures needed for life, such as cytoplasm and organelles. Mitosis and meiosis are different types of divisions and result in different numbers of daughter cells. (See Figure 4-4) Mitosis: This form of cell division occurs during rapidly during the formation of an embryo and during the early growth phases of life. As adults, our somatic cells continue to undergo mitosis to repair body tissues and replace cells that have stopped functioning efficiently. Prior to the mitotic division, the chromosomes replicate themselves, that is, they become double-stranded (in a human, this will result in 46 double-stranded chromosomes). This is followed by one cell division wherein the sister chromatids separate from each other, with one strand going into each daughter cell. The end result is two identical daughter cells with 46 (single-stranded) chromosomes each. The full complement of chromosomes, 46, is called the diploid number. Thus, in mitosis, the cell begins diploid and ends diploid. EXERCISE 6 Why is DNA replicated prior to mitosis? Meiosis: This process is more complicated than what occurs in mitosis. In meiosis, the genetic complement is cut in half so that each daughter cell has half the number of chromosomes as the original cell. Because of this, meiosis is often called a reduction division. The genetic complement is now half the original, meaning one copy of each chromosome pair ends up in each daughter cell. This is the haploid number. This process produces the gametes (sperm and ovum), and it takes place in the testes and ovaries, respectively. Two divisions, Meiosis I and Meiosis II, make this possible. Prior to meiosis, the chromosomes replicate themselves, again becoming double stranded. Thus, there are 46 double-stranded chromosomes when the Meiosis I stage begins. During Meiosis I, the homologous chromosomes pair up with each other, this sometimes results in intertwining. After the chromosome pairs have lined up across the center of the cell, the homologous pairs separate: one moves toward one daughter cell, while the other moves into the second daughter cell. The end result of Meiosis I is two daughter cells with 23 double-stranded chromosomes each. 68
Figure 4-4 A comparison of the processes of mitosis and meiosis. 69
In Meiosis II, each daughter cell divides again, resulting in four daughter cells total. In the nucleus, the sister chromatids separate, with one strand going into each daughter cell. This division is similar to mitosis. The result is four daughter cells, with half the number of original chromosomes (23 each). In males, this process is referred to as spermatogenesis and produces four haploid sperm cells. In females, this process is called oogenesis and produces one egg cell and three polar bodies. Although meiosis produces four cells with 23 chromosomes each, only the egg cell receives all of the cell contents from the cytokinesis (e.g. cytoplasm, ribosomes, etc.), and the polar bodies disintegrate. EXERCISE 7 Compare and contrast mitosis and meiosis in humans with the following matching questions. happens in the body cells produces 4 daughter cells begins with 46 chromosomes produces 2 daughter cells one nuclear division chromosome replication happens in the testes and ovaries daughter cells have 23 chromosomes each two nuclear divisions daughter cells are diploid a. mitosis b. meiosis c. both mitosis and meiosis Crossing Over Figure 4-5 The process of recombination (crossing over). 70
EXERCISE 8 Describe the difference between haploid and diploid cells and where they are found. _ Recombination (Crossing Over) During meiosis, an important event occurs that shuffles the genetic information around on the chromosomes. When the homologous chromosomes pair up and intertwine in Meiosis I, the chromatids break and portions of chromatids bearing genes for the same trait are exchanged, or reshuffled, between homologous chromosomes. This is called recombination, or crossing over (Figure 4-5). The end result may be that the original chromatids are carrying different alleles at that location. Crossing over allows a great amount of variability to be incorporated into the chromosome. EXERCISE 9 a.) Draw a homologous pair of chromosomes. Use one color (e.g., pink) for one member of the pair and use a second color (e.g., blue) for the second member of the pair. b.) Next, draw the two chromosomes crossing over, so that the two colors are touching. c.) Third, draw the two chromosomes after the crossing over is completed and they have shuffled their gene pairs, exchanging genes (colors) between them. Have at least one exchange. 71
EXERCISE 10 What do you think might happen if a cell underwent mitosis but not cytokinesis? EXERCISE 11 From a genetic standpoint, what is the significance of sexual reproduction? Figure 4-6 DNA structure 72
DNA Structure and Function In 1869, a chemist by the name of Friedrich Miescher found a substance in the cell nucleus that he called "nuclein." This substance became known as deoxyribonucleic acid, or DNA. In the 1950s, several researchers were attempting to discover the structure of DNA and exactly how it or some other molecule (e.g., proteins) might carry genetic information. In 1953, James Watson and Francis Crick proposed that the DNA molecule was composed of two strands that were twisted around each other in a double helix structure (like a twisted ladder). For their pioneering work, Watson and Crick were awarded the Nobel Prize in 1962 (Rosalind Franklin, who also worked on DNA structure, was also awarded the Nobel Prize that year; however, she died before the Nobel Prize was announced). It can be argued that the discovery of DNA as the genetic material and determination of its molecular structure are two of the most significant discoveries of the twentieth century. We now understand that DNA is made up of two chains of nucleotides. Each DNA nucleotide contains a phosphate, a sugar (deoxyribose sugar), and a base group (Figure 4-6). The phosphates and sugars make up the "sides" of the ladder-like structure. Each sugar is also connected to a base. The four possible bases are adenine (A), cytosine (C), guanine (G), and thymine (T). These bases join with each other in complementary base pairs to form the "rungs" of the ladder. The joining is very specific: A with T, C with G. Structurally and functionally, the base pairing lies at the heart of the DNA molecule. Because of this strict base pairing, the sequence of bases in the DNA molecule is preserved when the molecule is replicating or being copied. DNA has two main functions: (1) self-replication, which occurs when the cell is about to divide and (2) protein synthesis, or the formation of proteins. Proteins are structural molecules that are important for building all the cells of the body. Proteins also act as enzymes, allowing necessary chemical reactions in the body to take place. 73
Figure 4-7 DNA Replication DNA replication takes place just prior to cell division and results in the chromosomes producing copies of them (Figure 4-7). Replication begins when the DNA molecule "unwinds" and the strands separate. This results in two single strands of DNA with exposed bases. Free DNA nucleotides within the nucleus bond to the exposed bases, according to the base pairing rules, creating two new strands of DNA. Note that each new strand contains one original strand and one new strand. DNA replication is semiconservative: each parental strand remains intact, while a new complementary strand is formed. EXERCISE 12 What does it mean when we say DNA replication is semiconservative? 74
EXERCISE 13 a) Practice DNA base pairing: Consider the following DNA strand: A-T-C-C-T-A-G-G-T-C-A-G Identify the complementary bases:. b) Now, practice DNA replication. Consider the following double-stranded DNA molecule. Notice that the DNA bases are paired accordingly. Replicate the strands where they are separated. Protein Synthesis The sequence of bases in the DNA chain provides a code for amino acids, formerly once linked together form proteins. The process of protein synthesis occurs in two stages: (1) transcription, and (2) translation (Figure 4-8). First, in transcription, the DNA must be copied into a form that is able to exit the nucleus of the cell so it can travel to the ribosome. This is accomplished by copying itself into RNA (ribonucleic acid). RNA is a single-stranded molecule, composed of RNA nucleotides linked together. An RNA nucleotide is composed of a phosphate, a ribose sugar, and a base group. Note that the sugar molecules in DNA and RNA are slightly different. There are also differences in the bases. RNA contains A, C, and G, but it does not contain T. Instead, RNA has a base called uracil (U). The base pairing is similar: C with G and A with U. EXERCISE 14 Describe the differences in DNA and RNA structure. 75
The process of transcription begins with the DNA molecule unwinding and "unzipping" and the DNA strands again become separated. One DNA strand will be the template strand: the strand that is copied. This time, free RNA nucleotides in the nucleus will pair up with the exposed DNA bases on the template strand, following the base pairing rules. The strand of RNA that is formed is called messenger RNA or mrna because it carries the DNA "message" or code. The mrna strand may now exit the nucleus and head out to a specific organelle in the cytoplasm of the cell, called the ribosome, which is the site of protein synthesis. The DNA strands pair up again and rewind. EXERCISE 15 To transcribe means to make a copy of. Is an exact copy of DNA made during the process of transcription? Why or Why not? In the second stage, translation, the mrna code is scanned through the ribosome, where it is "read" like a bar code in a supermarket. "To translate" means to change from one language to another. In this process, the mrna code is translated into a strand of amino acids that will eventually form a protein. The ribosome reads the mrna strand three bases at a time. Each three bases in RNA are called a codon. Think of a codon like a three-letter word that codes for one amino acid. During the final part of translation, transfer RNA or trna carries an amino acid and sits at the ribosome, where it will be paired up with one of the mrna codons. As the codons are read by the ribosome, the appropriate amino acids are linked together in a long peptide chain. Many peptide chains linked together form a protein. EXERCISE 16 What happens in the ribosome during translation? 76
TRANSCRIPTION The two DNA strands separate at the site of a gene (the sequence of bases on one of the strands that carries the information to make a protein). The gene serves as a template to form a complementary mrna molecule that will carry the information to assemble a protein from the DNA in the nucleus to a ribosome in the cytoplasm. TRANSLATION (1) When the mrna binds to the ribosome, protein synthesis is initiated. As each codon in the mrna sequence is "read," a trna anticodon brings the corresponding amino acid to the ribosome. TRANSLATION (2) The mrna is read by the ribosome codon by codon. A second amino acid is brought to the ribosome by a trna, and it is linked to the first amino acid to start forming the polypeptide (or protein) chain. TRANSLATION (3) As each codon is read, trna transports the appropriate amino acid to the ribosome where it can be added to the growing protein chain. The ribosome moves down the mrna, codon by codon, until the end of the molecule is reached. At this point, the synthesis of one protein molecule is complete. Transcription Translation 77
Figure 4-8 The process of transcription and translation. Figure 4-9 List of amino acids and their abbreviations EXERCISE 17 The following chart lists all possible mrna codons and the 20 amino acids for which they code (see Figure 4-9 for abbreviations). Note that there is some redundancy in the code. Also note that some codons code for start or stop, which tells the cell where to start or stop making the protein. Using this information, fill in the blanks below the chart for the amino acid each codon calls for. UCA GUA UGG AGA CUC GCC CAU AUG 78
EXERCISE 18 For each of the following DNA strands 1) replicate the strand of DNA, 2) transcribe into mrna, 3) and translate into a protein chain. **Be sure to use the original DNA strand for both replication and transcription, and use the mrna codons when reading the chart to find the amino acids for the protein chain. a.) TAC-TGT-GCA-TCT-ATG-ACA-ACT Replicate DNA Transcribe into mrna Translate into amino acids b.) TAC-TGT-GCA-CTA-AAC-AAG-TAA-CAC-ATT Replicate DNA Transcribe into mrna Translate into amino acids 79
Mutations Mutations are errors that occur during DNA replication. Because of the redundancy in the coding of amino acids, most mutations do not have a profound effect on the phenotype of an individual. However, sometimes a simple point mutation (change in a single base) can result in a significant change to the whole process of protein synthesis. By altering one base, it can set off a chain of events which alters the mrna codon, and ultimately results in a different protein being produced. Other types of mutations include insertion mutations where a base (or series of bases) is repeated several times and deletion mutations where a base gets skipped during replication. EXERCISE 19 a. TAC-CTG-CGT-TTC-TAA-TGT Transcribe into mrna Translate into amino acids b. Next assume there was a point mutation and the first base was erroneously transcribed into a G. Transcribe into mrna Translate into amino acids c. Then assume there was a deletion mutation and the first base was skipped entirely. Transcribe into mrna Translate into amino acids d. Which type of mutation has a larger impact on protein synthesis? Why? 80