Module 1: DNA & RNA

Question 1

The Central Dogma of molecular biology

Answer 1

DNA makes RNA… RNA makes Proteins

The understanding that DNA is used to make RNA and RNA is used to make protein is known as the central dogma of molecular biology. In other words, it is central to everything we know about how information is used in the cell. We’ll explore the central dogma further in the next chapter.

Question 2

Nucleotides vs nucleic acids

Answer 2

Nucleotides are the subunit that is polymerized (connected into a long chain) to make nucleic acids (DNA and RNA)

Question 3

Nucleotides KEY CONCEPTS

Answer 3

Nucleic acids are polymers of nucleotides. A nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups. DNA contains adenine, guanine, cytosine, and thymine deoxyribonucleotides, whereas RNA contains adenine, guanine, cytosine, and uracil ribonucleotides. DNA is double-stranded and forms a double helix structure that allows for information storage. Prior to dividing , a cell copies all of its DNA using DNA replication to ensure all new cells have the DNA they need. DNA Replication involves the formation of a replication fork, addition of RNA primers to create a “handle” for DNA polymerase, synthesis of the new DNA strand by DNA polymerase, and sealing the DNA backbone by DNA ligase. RNA is single-stranded and is grouped into three types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). All three types of RNA play an important role in the central dogma.

Question 4

Nucleic acids are polymers of nucleotides.

Answer 4

A nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups. DNA contains adenine, guanine, cytosine, and thymine deoxyribonucleotides, whereas RNA contains adenine, guanine, cytosine, and uracil ribonucleotides. DNA is double-stranded and forms a double helix structure that allows for information storage. Prior to dividing , a cell copies all of its DNA using DNA replication to ensure all new cells have the DNA they need. DNA Replication involves the formation of a replication fork, addition of RNA primers to create a “handle” for DNA polymerase, synthesis of the new DNA strand by DNA polymerase, and sealing the DNA backbone by DNA ligase. RNA is single-stranded and is grouped into three types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). All three types of RNA play an important role in the central dogma.

Question 5

What does a nucleotide consist of?

Answer 5

A nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups.

Question 6

What nucleotides are contained in DNA?

Answer 6

DNA contains adenine, guanine, cytosine, and thymine deoxyribonucleotides,

Question 7

What nucleotides are contained in RNA?

Answer 7

RNA contains adenine, guanine, cytosine, and uracil ribonucleotides.

Question 8

What is the structure of DNA?

Answer 8

DNA is double-stranded and forms a double helix structure that allows for information storage.

Question 9

How is DNA in all cells as cells divide?

Answer 9

Prior to dividing , a cell copies all of its DNA using DNA replication to ensure all new cells have the DNA they need.

Question 10

DNA replication quick overview (4 steps)

Answer 10

DNA Replication involves the formation of a replication fork, addition of RNA primers to create a “handle” for DNA polymerase, synthesis of the new DNA strand by DNA polymerase, and sealing the DNA backbone by DNA ligase.

1. Fork
2. RNA primers
3. DNA polymerase synthesizes a new strand
4. Ligase seals the DNA.

Question 11

What is the structure of RNA?

Answer 11

RNA is single-stranded

Question 12

Whate are the 3 types of RNA?

Answer 12

three types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). All three types of RNA play an important role in the central dogma.

Question 13

Nucleic acids

Answer 13

are polymers of nucleotides.

Question 14

DNA is a Double Helix

Answer 14

As demonstrated by the animation at the beginning of this section, DNA contains two polynucleotide strands whose bases pair in a predictable way through hydrogen bonding. Adenine (A) always pairs with thymine (T), and cytosine (C) always pairs with guanine (G). The A and T are linked by two hydrogen bonds, while C and G are linked by three hydrogen bonds, as shown below. Additionally, the two strands are antiparallel, which means they have opposite 5’ and 3’ orientations, similar to a two-way street in which traffic is oriented in opposite directions.

Question 15

What kind of strands make up the DNA double helix and how are they bonded?

Answer 15

DNA contains two polynucleotide strands whose bases pair in a predictable way through hydrogen bonding.

Question 16

Which base does each of the nucleotide bases pair with?

Answer 16

Adenine (A) always pairs with thymine (T), and cytosine (C) always pairs with guanine (G).

Question 17

What kind of bonds are between the nucleotide bases?

Answer 17

The A and T are linked by two hydrogen bonds, while C and G are linked by three hydrogen bonds

Question 18

Explain the antiparallel nature of the

Answer 18

the two strands are antiparallel, which means they have opposite 5’ and 3’ orientations, similar to a two-way street in which traffic is oriented in opposite directions.

Question 19

DNA Replication - The Structure of DNA Allows it to be Copied

Answer 19

When Watson and Crick discovered that the structure of DNA was a double helix, they immediately understood why its structure was important to its function. Each type of nucleotide only pairs with one other nucleotide (C only pairs with G, for example), so knowing the information from one strand means we know its complementary sequence as well. Thus, each strand of parental (“old”) DNA can be separated and act as a template for the synthesis of a complementary daughter (“new”) strand. This allows the parental DNA to generate two complete, semi-conservative copies of DNA. The term semi-conservative means that each copy contains an “old” strand and a “new” strand (Figure 1-5). The process of copying the DNA is known as DNA replication. DNA replication allows each cell (and each person) to pass on a complete set of DNA to the next generation.

Question 20

Who discovered the double helix structure of DNA?

Answer 20

Watson and Crick

Question 21

What is DNA replication?

Answer 21

The process of copying DNA.

Question 22

When DNA is replicated, why are the strands called “semi-conservative?

Answer 22

info from one strand means we know its complementary sequence as well. Thus, each strand of parental (“old”) DNA can be separated and act as a template for the synthesis of a complementary daughter (“new”) strand. This allows the parental DNA to generate two complete, semi-conservative copies of DNA. The term semi-conservative means that each copy contains an “old” strand and a “new” strand… DNA replication allows each cell (and each person) to pass on a complete set of DNA to the next generation.

Question 23

Okazaki fragments

Answer 23

RNA primers are used at several places along the two strands of DNA, which means the new DNA is created in fragments (known as Okazaki fragments for the person who discovered them). However, RNA is much less stable than DNA, and needs to removed to prevent degradation. As each Okazaki fragment is finished, the RNA primer is removed by RNase H and replaced with DNA by DNA polymerase. This process leaves nicks in the sugar-phosphate backbone of the DNA. DNA ligase seals the nicks to create a continuous strand of new DNA (Figure 1-8).

Question 24

DNA Polymerase Proofreads Newly Synthesized DNA

Answer 24

DNA replication is remarkably reliable, incorporating an erroneous base only once for about every million base pairs. If the wrong nucleotide does get incorporated into the growing DNA strand, the polymerase can detect the distortion it creates in the double helix. Luckily, DNA polymerase has a proofreading activity that can remove erroneous nucleotides at the 3’ end of the new DNA strand. This activity is known as a 3’ → 5’ exonuclease (“exo” means end and “nuclease” means nucleotide removal) because it removes nucleotides from the 3’ end of the DNA (Fig. 1-9).

Question 25

DNA polymerase and exonuclease

Answer 25

has a proofreading activity that can remove erroneous nucleotides at the 3’ end of the new DNA strand.

This activity is known as a 3’ → 5’ exonuclease (“exo” means end and “nuclease” means nucleotide removal) because it removes nucleotides from the 3’ end of the DNA (Fig. 1-9).

Question 26

RNA is a Single Strand

Answer 26

RNA, which is a single-stranded nucleic acid polymer, has greater freedom of movement than DNA, whose structure is constrained by the requirements of regular base pairing between its two strands. An RNA strand can fold back on itself, forming base pairs between the complementary segments of the same strand. The simplest example is a stem loop, as demonstrated in Figure 1-10. Thus, RNA is seldom a straight chain, but instead takes on different shapes depending on its sequence. This conformational freedom is important for the variety of structures and roles that RNA has in the cell.

Question 27

Three Types of RNA

Answer 27

There are three types of RNA in the cell: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Each type of RNA is essential to the flow of information in the cell and are part of the central dogma, as shown in Figure 1-11.

Question 28

Transcription and Translation: A Closer Look KEY CONCEPTS

Answer 28

Genes are segments of DNA sequence that code for a particular product, usually a protein. Mutated genes can lead to changes in the protein and cause disease. Transcription is the process by which the DNA sequence of a gene is copied into mRNA by RNA polymerase, and it is the first step of gene expression. Gene expression is at least partially controlled by promoters and transcription factors that recruit RNA polymerase to a gene. The mRNA transcripts are processed prior to translation. Translation is the process of protein synthesis by the ribosome using the sequence information in mRNA. During translation, the ribosome matches the codon sequence of the mRNA with the anticodon of the corresponding tRNA to ensure the correct amino acid is added to the protein. Amino acids are added to the growing protein with peptide bonds.

Question 29

Transcription

Answer 29

To transcribe a gene, one of the two strands of DNA serves as a template for making a complementary strand of RNA. The RNA, therefore, has the same sequence (except for the substitution of U for T) and the same 5’ -> 3’ orientation as the nontemplate strand of DNA. This strand of DNA is called the coding strand, and the template strand is called the noncoding strand. Thus, the coding strand of DNA gives the sequence of the RNA to be made, but the template strand is the DNA strand used to make the RNA.

Question 30

Transcription

Answer 30

To transcribe a gene, one of the two strands of DNA serves as a template for making a complementary strand of RNA. The RNA, therefore, has the same sequence (except for the substitution of U for T) and the same 5’ -> 3’ orientation as the nontemplate strand of DNA. This strand of DNA is called the coding strand, and the template strand is called the noncoding strand. Thus, the coding strand of DNA gives the sequence of the RNA to be made, but the template strand is the DNA strand used to make the RNA.

Question 31

Transcription Begins at Promoters

Answer 31

The initiation of RNA synthesis requires a specific DNA sequence at a site known as a promoter. The promoter is located near the transcription start site before the start of the gene. The DNA sequence at the promoter is recognized by specific proteins called transcription factors, which recruit RNA polymerase to the transcription start site. RNA polymerase separates the two DNA strands in a small portion of the DNA molecule to form a transcription bubble, thus allowing it to access the template strand and begin RNA synthesis. RNA polymerase then creates a short DNA-RNA hybrid at its center that matches the correct RNA nucleotides to the DNA sequence it is transcribing. Once the RNA is finished being made, the newly synthesized RNA is released as a single-stranded molecule.

Question 32

mRNA Transcripts are Processed Prior to Translation

Answer 32

Both during and after transcription, RNA is processed to generate a mature, functional form of RNA. This processing includes putting a “cap” on the 5’ end and a polyadenylated (poly-A) “tail” at the 3’ end. The 5’ cap is added to the 5’ end of the nascent RNA during transcription, but the poly-A tail is added to the 3’ end of the RNA only after transcription termination. Additionally, all human genes undergo a process known as splicing, in which portions of the sequence called introns (intervening sequences) are cut out, and the remaining portions of the gene (expressed sequences, or exons) are joined together. Once splicing is complete, the mature, fully-processed RNA is ready for translation.

Question 33

Alternative Splicing Increases Variation in Gene Expression

Answer 33

Introns typically comprise over 90% of a gene’s total length, which means that a lot of RNA must be transcribed and then discarded. Additionally, the complexity of the splicing process creates many opportunities for things to go wrong: a majority of mutations linked to inherited diseases involve defective splicing. So, just what is the advantage of arranging a gene as a set of exons separated by introns? One answer to this question is that splicing allows cells to increase variation in gene expression through alternative splicing. At least 95% of human protein-coding genes exhibit splice variants. Variations in splicing can include skipping particular exons or retaining an intron. Thus, certain exons present in the gene may or may not be included in the mature RNA transcript (Fig.1-15).

Question 34

Gene Expression and Regulation

Answer 34

Every cell in your body (except reproductive cells) contains an identical set of chromosomes–the exact same set of DNA molecules-yet your cells are not all alike. In fact, cellular processes that are critical to one set of cells (those that produce insulin in your pancreas, for example) play no role whatsoever elsewhere. The genetic coding for making insulin is contained in every cell in your body but only expressed or “turned on” in a few. How do the cells in the pancreas ‘know” that they are supposed to activate the particular gene for insulin while the cells in the brain know they are not supposed to? The mystery of DNA’s operation runs even deeper than this. It now appears that only about 5% of all DNA in human beings is actually taken up by the genes. The other 95% used to be called “junk DNA” because nobody understood why it was there. Scientists are increasingly coming to believe, however, that at least some of that DNA contains instructions for gene expression. Many scientists believe that the failure or mutation of these instructions leads to disease such as cancer. If a cell is dividing and the mechanism that tells the cell when it’s time to stop is faulty, the cell may continue to multiply and produce a tumor. Damage to the control mechanisms in a cell may therefore be even more serious than damage to the genes themselves.

Question 35

Translation

Answer 35

Once a messenger RNA (mRNA) has been transcribed and processed in the nucleus, it leaves the nucleus and is used to translate the nucleic acid “language” of nucleotides to the protein “language” of amino acids. Quite appropriately, this process is known as translation. During translation, the ribosome, a large molecular machine, brings the three types of RNA together to make a protein. The rRNA is part of the ribosome itself (along with ribosomal proteins), and it binds to the mRNA made during transcription. The transfer RNA (tRNA) molecules also bind to the ribosome, and they ensure the correct sequence of amino acids for a protein based on the mRNA sequence.

Question 36

Using the Genetic Code

Answer 36

The correspondence between amino acids and mRNA codons is known as the genetic code. (Technically codons also exist in DNA, they are just sequences of three nucleotides, but since DNA is not used in translation the code is almost always written to correspond to RNA.) There are a total of 64 codons: 3 of these are “stop” signals that terminate translation, and the remaining 61 represent, with some redundancy, the 20 standard amino acids found in proteins. Table 1.1 shows which codons specify which amino acid.

Question 37

DNA Damage and Repair KEY CONCEPTS

Answer 37

A mutation in DNA can arise from DNA replication errors, by-products of cellular processes, and environmental factors. A variety of DNA repair pathways enable the cell to remove and repair many mutations that arise in the DNA. Base Excision Repair pathways repair damaged, single bases in the DNA. Nucleotide Excision Repair pathways repair damage that involves multiple nucleotides, such as thymine dimers. Mismatch Repair pathways correct mismatches resulting from DNA polymerase errors during replication. Homologous Recombination and Non-homologous end-joining are used to repair double-stranded DNA breaks. Mutations in the genes of DNA repair pathways can lead to accumulation of mutations, ultimately leading to cancer.

Question 38

DNA is Damaged in Many Ways

Answer 38

DNA in cells is constantly being damaged by a variety of chemicals, both those resulting from normal cellular activity as well as environmental factors. Damage to DNA can block essential processes including DNA replication and transcription and can lead to mutations. Common sources of DNA damage include the following: Ultraviolet (UV) radiation can cause adjacent T bases to fuse together to form a thymine dimer that blocks DNA replication and transcription. Ionizing radiation, such as X-rays and radioactive decay, can cause strand breaks as well as create reactive oxygen species that damage the bases. Chemicals that are carcinogens or mutagens alter the structure of DNA bases. Reactive oxygen species generated by processes in the cell can damage the DNA bases. Additionally, many chemotherapeutic agents attack DNA. Some change the structure of individual bases while others, such as cisplatin, cross-link the two DNA strands together. The higher sensitivity of replicating cells to DNA damage means that rapidly dividing tumor cells are more sensitive to these damaging agents than are normal cells, but their damage to normal cells limits their dosing and use.

Question 39

Types of Mutations

Answer 39

Mutations are heritable changes in the DNA sequence. They can result from replication errors, from damage to the DNA, or from errors introduced during repair of damage. Mutations that are changes of a single base pair are called point mutations. Several kinds of point mutations are possible, and point mutations can be categorized by their effect on a coding sequence. Silent mutations are point mutations that result in no change in amino acid sequence due to some redundancy in the genetic code. For example, the codon UCU could have point mutations to UCC, UCA, or UCG and still code for the same amino acid, serine. Missense mutations are point mutations that change a single base pair in a codon such that the codon now encodes a different amino acid (Figure 1-10 a). Nonsense mutations are point mutations that change a single base pair in a codon to a stop codon that terminates translation (Figure 1-10 b). Nonsense mutations usually have more severe effects than missense mutations because they lead to synthesis of truncated (and generally unstable) polypeptides. Silent or synonymous mutations do not alter the amino acid encoded; these include many changes in the third nucleotide of a codon. Some silent mutations may, however, have serious consequences if they alter the splicing pattern of the gene.

Question 40

Mutated Genes Can Cause Disease

Answer 40

As discussed in the chapter on Genes to Proteins, the DNA sequence of a gene determines the resulting protein sequence. Therefore, changes to the DNA sequence, whether from damage or replication mistakes by DNA polymerase, can lead to changes in the protein sequence. Sometimes, these changes result in disease. For example, the variant hemoglobin protein that causes sickle cell anemia results from a point (missense) mutation that changes the normal GAG codon to GTG, as shown below. This results in the substitution of the amino acid glutamate with the amino acid valine with serious consequences for those who carry this change in their DNA.

Question 41

DNA Repair

Answer 41

Due to consistent damage of DNA by the sources described above, maintenance of the genetic information requires constant repair of damaged DNA. All free living organisms have several mechanisms to repair damage to DNA. A key feature in most repair processes is the double-stranded nature of DNA, which allows restoration of the correct sequence on a damaged strand using the complementary genetic information on the other strand.

Question 42

Excision Repair Corrects the Most Frequent DNA Lesions

Answer 42

Excision repair is a general mechanism that can very accurately repair many different kinds of damage. There are two major modes of excision repair: base excision repair (BER) and nucleotide excision repair (NER). The basic steps for both of these modes of repair include: Recognize the damage Remove the damage by excising part of one strand to leave a gap Resynthesize the sequence using genetic information from the other strand to fill the gap Ligate to restore continuity of the DNA backbone. Several repair enzymes aid in the excision repair processes. The major difference between the two kinds of repair is how many nucleotides are removed. In base excision repair a single nucleotide is replaced (see Figure 1-21), while in NER, several nucleotides, usually around 30, are removed and replaced (see Figure 1-22).

Question 43

Mismatch Repair

Answer 43

Mismatch repair takes place soon after DNA replication to remove any replication errors. Mismatches are not like DNA damage: there is no damaged or modified base present, just the wrong one of the four bases. The recognition of mismatches relies on the distortion of the double-helical structure. A major difference between repair of DNA damage and repair of mismatches is in the choice of which base to remove. Enzymes can recognize damaged bases specifically and remove them, either individually or as part of an oligonucleotide. But when a mismatch is recognized, both bases are normal; which one should be removed? In newly replicated DNA, removing the newly synthesized base would preserve the genetic information, whereas removing the base from the parental strand would permanently alter the DNA sequence, producing a mutation. Luckily, the cell has reliable ways to distinguish newly synthesized DNA from the parental DNA and reliably remove the erroneous base.

Question 44

Mismatch Repair

Answer 44

Mismatch repair takes place soon after DNA replication to remove any replication errors. Mismatches are not like DNA damage: there is no damaged or modified base present, just the wrong one of the four bases. The recognition of mismatches relies on the distortion of the double-helical structure. A major difference between repair of DNA damage and repair of mismatches is in the choice of which base to remove. Enzymes can recognize damaged bases specifically and remove them, either individually or as part of an oligonucleotide. But when a mismatch is recognized, both bases are normal; which one should be removed? In newly replicated DNA, removing the newly synthesized base would preserve the genetic information, whereas removing the base from the parental strand would permanently alter the DNA sequence, producing a mutation. Luckily, the cell has reliable ways to distinguish newly synthesized DNA from the parental DNA and reliably remove the erroneous base.

Question 45

Homologous Recombination For Repair and Diversity

Answer 45

Certain types of irradiation, such as exposure to X-rays or radioactivity, can completely sever the strands of a DNA double helix, leading to a double-strand break. These breaks, and other types of severe damage, can be re-joined through a process of recombination, called homologous recombination. When recombination takes place as a repair mechanism, the recombination machinery locates the DNA sequence that has homology (nearly identical sequence) to both sides of the lesion and then uses the sequence of the intact DNA strands to fix the double-strand break. The process results in some of the sequence from the broken strand being incorporated into the intact strand, and vice versa. The DNA from both strands essentially becomes mixed, but if the sequences were highly homologous (basically identical), then the gene sequences are not affected (see Figure 1-24).

Question 46

Inheritance KEY CONCEPTS

Answer 46

Genes are located on chromosomes and come in pairs in most human cells. Each member of a gene pair (each copy of the gene) is known as an allele. Genes are passed on from one generation to the other. The genotype (pair of genes) decide the phenotype (observable characteristics) of an individual. Inheritance is the passage of hereditary traits from one generation to the next. It is the process by which you acquired your characteristics from your biological parents and may transmit some of your traits to your children. Common inheritance patterns include: complete dominance, incomplete dominance, codominance, and sex-linked (X-linked) traits. The genetic material of a father and mother unite when a sperm cell fuses with an egg to form a zygote. Children resemble their biological parents because they inherit traits passed down from both parents in their DNA. We now examine some of the principles involved in that process, called inheritance. The branch of biology that studies inheritance is called genetics. The area of health care that offers advice on genetic problems (or potential problems) is called genetic counseling.

Question 47

DNA is Organized into Chromosomes

Answer 47

If our genes are a way that DNA organizes itself, then our chromosomes are our genes’ way of organizing themselves. As discussed in the chapter “Genes to Proteins” above, genes are sections of DNA that code for a protein and are expressed (transcribed and translated) depending on the needs of the cell. However, each human cell has over 3 billion base pairs of DNA and ~20,000 genes! How does the cell organize the DNA in a way that prevents it from becoming a tangled mess and allows it to locate the needed gene at the needed time? DNA is wrapped around proteins called histones to prevent tangling, and the combination of DNA and histone proteins creates nucleosomes. The histones promote coiling of the nucleosomes into a larger chromatin fiber. The chromatin fibers are folded into large loops that eventually form chromosomes. The chromosomes are highly compact DNA, and they also serve as a kind of multilevel filing system for the genes–specific genes are located at specific sites on particular chromosomes (i.e., the gene for hemoglobin is always found on chromosome 11). This allows the cell to easily locate the genes it needs at any given time.

Question 48

Our Chromosomes Come in Pairs

Answer 48

Genes are located on chromosomes. Human beings have 23 pairs of chromosomes (46 total) and these are conveniently numbered 1 - 22, for the non-sex chromosomes. The chromosomes that make up the last pair are called X and y. These are the sex chromosomes. In mammals, females have two X chromosomes and males have an X and a y chromosome. We inherit one chromosome of each pair from our biological father and one from our biological mother. The gametes (egg and sperm cells) contributed by each biological parent have only 23 chromosomes, one from each pair, and the chromosomes from both the egg and sperm together provide the full set of 46 chromosomes to their offspring.

Question 49

Phenotype and Genotype

Answer 49

We all have the same basic arrangement of genes in our chromosomes, despite individual differences in phenotype. The phenotype is all the observable characteristics or traits of an individual, including ones that are not easily seen, such as blood type or color blindness. These phenotypic differences emerge from subtle differences in genotype–our complete set of genes–as well as environmental factors. Our phenotype is the result of our genotype and all the environmental influences on us, including the quality of our food, the type of shelter we live in, and even our financial security.

Question 50

Alleles Are Gene Variations

Answer 50

Genes are found in specific locations on their chromosomes. We know that chromosomes come in pairs, which means genes come in pairs as well. Each member of the gene pair is called an allele, and the members can be identical to each other or slightly different. An allele is an alternative form of a gene. It is the differences in alleles that give rise to different genotypes. Alleles may have differences in the sequences of only one or a few DNA base pairs, but that small difference means they produce different proteins than their counterpart genes. The very small difference (less than 1%) in genotype between you and your neighbor is because of slightly different alleles, which combine to give rise to some very different phenotypes. We have seen that each somatic cell (any cell that isn’t a gamete) contains two copies of every allele, one obtained from each biological parent. When the two alleles are identical, the genotype is homozygous for the trait that is controlled by those alleles. If the two alleles code for two variations of that trait the genotype is heterozygous.

Question 51

Representing the Inheritance of Alleles

Answer 51

Visualizing and predicting how different alleles will be inherited based on the genetics of the parents is an important aspect of understanding inheritance. The relationship of genes to heredity is illustrated by examining the alleles involved in a disorder called phenylketonuria (PKU). People with PKU are unable to manufacture the enzyme phenylalanine hydroxylase and are therefore unable to metabolize the amino acid phenylalanine. The normal allele that codes for phenylalanine hydroxylase is symbolized as P; the mutated allele that fails to produce a functional enzyme is represented by p. The following chart, which shows the possible combinations of gametes from two heterozygous parents who each have one P and one p allele, is called a Punnett square. In constructing a Punnett square, the possible paternal alleles in sperm are written at the left side and the possible maternal alleles in eggs are written at the top. The four spaces on the chart show how the alleles can combine in zygotes formed by the union of these sperm and eggs to produce the three different combinations of genes, or genotypes.

Question 52

Complete Dominance is a Small Part of Our Phenotype

Answer 52

As discussed above, only homozygous recessive individuals express a recessive phenotype. If one allele is dominant, the dominant phenotype must be expressed. This means that if your appearance includes a recessive trait, all of your gametes (eggs or sperm) carry only the recessive allele. You are homozygous recessive for that trait. If that trait is dominant in your phenotype, you could be homozygous dominant or heterozygous, and it is hard to predict which allele your gametes will carry. This type of complete dominance is only a small part of our overall phenotype because relatively few traits are controlled by a single set of alleles with a complete dominance pattern. Table 1-3 below indicates some of these characteristics in humans:

Question 53

Incomplete Dominance and Codominance Complicate the Picture

Answer 53

Many traits in humans exhibit incomplete dominance or codominance rather than the complete dominance found by Mendel (and discussed above). This is due to the fact that many traits result not from one gene dominating another but from several genes affecting the phenotype simultaneously. Additionally, many traits are multifactorial, meaning they arise from the interactions of several genes and environmental influences. Traits such as height and body type are multifactorial traits. Incomplete dominance tends to produce different phenotypes based on the combination of alleles present in the heterozygotes. Unlike complete dominance, in which there are only two possible phenotypes (the dominant and the recessive phenotypes), incomplete dominance traits have a distinct phenotype for the heterozygous genotype. One example of this in humans is hair pattern. There are two different alleles for this trait: H for curly and H’ for straight. Individuals with a HH genotype will have curly hair, a H’H’ genotype produces straight hair, and the heterozygous genotype HH’ produces wavy hair–its own, distinct phenotype that is often a blending of the two homozygous phenotypes.

Question 54

Sex-Linked Inheritance

Answer 54

In addition to determining the biological sex of the offspring, the sex chromosomes are responsible for the transmission of several nonsexual traits. Inheritance of genes located on the sex chromosomes show sex-linked inheritance because their inheritance patterns differ between males and females. Many genes for sex-linked traits are present on X chromosomes but are absent from Y chromosomes, so males (XY) have only one copy of the alleles found on the X chromosome. This feature produces a pattern of heredity called X-linked inheritance, the most common type of sex-linked inheritance. While Y-linked inheritance is possible, it is extremely rare because the Y chromosome is small and doesn’t carry many genes. One example of sex-linked inheritance is red-green color blindness, the most common type of color blindness. This condition is characterized by defects in one of the opsin genes that cause a deficiency in either red- or green-sensitive cones. As a result, red and green are seen as the same color (either red or green, depending on which cone is present). The gene for red-green color blindness is a recessive one designated Xc. Normal color vision, designated XC, dominates. The C/c genes are located only on the X chromosome, so the ability to see colors depends entirely on the X chromosomes. The possible combinations are as follows:

Question 55

PCR and Genetic Testing KEY CONCEPTS

Answer 55

Polymerase Chain Reaction (PCR) is a tool used to amplify a specific segment of DNA. Genetic testing utilizes PCR to identify potential sources of genetic disease in an individual or their offspring. The type of PCR product generated provides information about the specific mutation and its accompanying phenotype. With the knowledge that DNA contains our genetic information came the desire to know the exact sequence of that genetic information, particularly with regards to disease genes that can be passed down from parents to offspring. Determining the sequence of even a short DNA sequence was extremely laborious for many decades, and only short sequences could be determined. This all changed with the invention of the polymerase chain reaction (PCR) in 1985 by Kary Mullis. This method has turned DNA sequencing into a fast, routine, and inexpensive process that allows for accurate genetic testing of individuals for a variety of reasons.

Question 56

Polymerase Chain Reaction (PCR) Amplifies Selected DNA Sequences

Answer 56

Polymerase Chain Reaction (PCR) is a technique that copies a chosen segment of DNA. It is similar to making a copy on a copy machine. Just as an important page in a book can be selectively copied, PCR allows us to make many copies of an important gene or other DNA sequence. In the case of genetic testing, the “important pages” are the genes that underlie disease. To learn about how PCR works, and how it’s used in genetic testing, watch the video below.

Question 57

Genetic Testing Uses PCR

Answer 57

Genetic testing involves determining the sequence of one or more segments of an individual’s DNA for medical, forensic, or scientific purposes. Because the samples of DNA at a crime scene or available from an ancient bone sample can be minuscule, PCR amplification has become an indispensable tool in genetic testing. Forensically, the DNA from a single hair or sperm can be amplified by PCR so that it can be used to identify the donor. Traditional ABO blood-type analysis requires a coin-sized drop of blood; PCR is effective on pinhead-sized samples of biological fluids. Courts now consider DNA sequences as unambiguous identifiers of individuals, as are fingerprints, because the chance of two individuals sharing extended sequences of DNA is typically one in a million or more. In a few cases, PCR has dramatically restored justice to convicts who were released from prison on the basis of PCR results that proved their innocence—even many years after the crime-scene evidence had been collected. Clinically, genetic testing by PCR is used to diagnose infectious diseases and to detect rare pathological events, such as mutations leading to cancer. Genetic testing can also determine the genotypes of two parents for debilitating diseases, such as cytic fibrosis, which allows them to make informed decisions regarding their reproduction.

Question 58

PCR Products Can Identify Specific Types of Mutations

Answer 58

Individuals with genetic diseases harbor differences that can often be detected using PCR. For example, individuals with Huntington’s disease have extra repetitive segments of DNA that make their huntingtin gene longer than the normal sequence. If someone with Huntington’s disease undergoes genetic testing, their huntingtin gene will yield a longer PCR product, and this difference in length can be easily identified. Similarly, if a mutation had caused a large deletion in the gene, the PCR product of that gene will be shorter than the normal gene. Determining a particular mutation, especially a point mutation, can be done by designing primers that are complementary to the mutated sequence. When the primers are designed this way, a PCR product is only produced if the genes contains the designated mutation. This technique has been used for identifying particular mutations in the promoter of the BRCA1 gene that are linked to heritable breast cancer. Knowing the particular mutation in a gene linked to disease can provide information about the expected phenotype. For example, the cftr gene associated with cystic fibrosis (CF) has over 1000 known mutations, but less than 150 of those mutations lead to CF. Thus, identifying the specific mutation can have clinical implications. In addition to designing primers to identify a single, targeted mutation, as in the case of BRCA1, the entire gene sequence can be amplified and the PCR product sequenced to determine the entire gene sequence, including any mutations present. This allows the detection of multiple mutations as well as mutations that have not been identified previously.