Chapter 11

11
KEY KNOWLEDGE
Gene function: genes in action

recognise that, while most genes code for proteins, some genes just produce RNA become aware that changes in a gene may involve the coding region or anking regions develop knowledge of DNA as a selfreplicating molecule recognise the relationship between genotype and phenotype in terms of gene action.
This chapter is designed to enable students to: extend awareness that DNA is an informationcarrying molecule and can transfer its coded information to RNA develop knowledge of the location and principal events in the process of transcription develop knowledge of the location and principal events in the process of translation
Figure 11.1 These cobs of corn (Zea mays) show the action
of several genes. One gene acts to control the production of pigment on the outer layer of each kernel, while another acts to control the colour of any pigment that is produced. Yet another gene acts to control the chemical nature of the endosperm
NATURE OF BIOLOGY BOOK 1
384
contained within each kernel. In this chapter, we will explore how the action of genes (see centre image) is achieved through the processes of transcription and translation, and how the genetic material, DNA, replicates. We will also examine how gene action is controlled and how genes can be selectively silenced.
Sea in the blood

For many hundreds of years, a childhood disease known as sea in the blood or thalassaemia (thalassa = sea; haima = blood) has been prevalent in Mediterranean countries and in a broad region extending across the Middle East and South-East Asia. During their rst year of life, affected babies showed the anaemia that is characteristic of the sea in the blood disorder. In the past, in the absence of any treatment for the disorder, other symptoms followed and death usually occurred in early childhood. We know this disorder now as beta thalassaemia.
Meet a family and its genes

Giovanni, just in his teens, has the inherited disorder, beta thalassaemia. This disorder was diagnosed when he was a young child. The red blood cells in Giovannis bloodstream are smaller than usual and do not contain the usual amount of haemoglobins (see gure 11.2). As a result, Giovannis red blood cells do not survive in his circulatory system as long as normal (this is usually about four months).
Figure 11.2 Photomicrograph

of blood cells from a person with thalassaemia. The red blood cells are pale because they contain less than normal amounts of haemoglobin, the red oxygen-carrying pigment. The blood cells are smaller than normal and many are deformed.
Mrs C Mr C
Giovanni C
Maria C
Figure 11.3 In this family only

Giovanni has the inherited disorder thalassaemia. Who must be carriers?
Beta thalassaemia is a recessive disorder that occurs in both sexes, and is seen mainly in people of Mediterranean, Indian and South-East Asian origin. Giovannis parents, who are distantly related, are both carriers of the disorder but are unaffected by the disorder. Giovannis younger sister, Maria, does not have beta thalassaemia, nor is she a carrier of the disorder (see gure 11.3). Although Giovanni is the only member of his immediate family who has beta thalassaemia, a few of his other relatives also had this disorder.
Haemoglobin and its chains

ODD FACT
The haemoglobin in a normal newborn is about 70 per cent haemoglobin F and about 30 per cent haemoglobin A. By the end of the rst year of its life, all the fetal haemoglobin has been replaced by haemoglobin A.
Haemoglobins are compounds that transport oxygen in red blood cells. About 98 per cent of the haemoglobin typically found in human red blood cells by 12 months after birth is a type known as haemoglobin A. The remaining two per cent is mainly haemoglobin A2. Traces of haemoglobin F are also found. All haemoglobins are composed of four protein chains and iron-containing haem molecules. Table 11.1 shows the protein chains present in various haemoglobins (the chains are identied by letters of the Greek alphabet). In haemoglobin A, the four protein chains consist of two alpha chains and two beta chains. In haemoglobin A2, the chains consist of two alpha and two delta chains. Giovanni cannot produce beta chains and so has no haemoglobin A. His red blood cells contain abnormally high amounts of haemoglobin A2.
GENE FUNCTION: GENES IN ACTION
385
Table 11.1 Chains present in

various types of haemoglobins. How might this information assist a forensic scientist to distinguish adult blood from fetal blood?
Type of haemoglobin haemoglobin A
Usual occurrence major post-birth haemoglobin
Chains present 2 alpha chains 2 beta chains
Genes involved HBA gene on chromosome 16 HBB gene on chromosome 11 HBA gene on chromosome 16 HBA gene on chromosome 11 HBA gene on chromosome 16 HBG gene on chromosome 11
haemoglobin A2
minor post-birth haemoglobin
2 alpha chains 2 delta chains
haemoglobin F
major fetal haemoglobin
2 alpha chains 2 gamma chains
Symptoms of beta thalassaemia

People with beta thalassaemia tend to suffer from anaemia because their red blood cells have an abnormally short life. Giovanni sometimes tires easily because he has a reduced oxygen supply to his tissues. Other signs of thalassaemia include an enlarged liver and spleen and an expansion of the bone marrow that can lead to deformity of skull bones. As red blood cells age, they eventually die. Normally, a persons body is able to cope with the iron and other breakdown products of haemoglobin. However, because the red blood cells of people with thalassaemia die more rapidly, their bodies tend to become overloaded with breakdown products of haemoglobin that they cannot excrete fast enough. This results in abnormal deposition of iron in the cells of their kidneys, heart, brain and other organs another symptom of the disorder.
Figure 11.4 A slow-infusion pump

slowly delivers a measured dose of an iron-binding agent, Desferal, through a needle inserted below the skin. This battery-driven pump is usually worn at night. In this case, the person shown is about to use the pump when he is receiving a blood transfusion.
Treating beta thalassaemia

Giovanni will receive life-long treatment for the major symptoms of his disorder. Each night, he takes a drug, Desferal, that binds to the excess iron and removes it from his system. Desferal is injected through a slow-infusion pump that he wears attached to his body at night (see gure 11.4). Every six weeks or so, Giovanni travels to a Day Transfusion Centre at a large city hospital where he receives a blood transfusion to deal with the anaemia. Giovanni received his rst transfusion at 10 months of age and began Desferal treatment when he was four-and-a-half years old. What is the inherited difference between Giovanni and his sister, Maria, that causes him to need lifetime treatment for beta thalassaemia, while his sister is free of this disorder? To answer this question, we must look at the DNA of one gene.
The HBB gene

Giovanni and Maria differ in one of their genes, known as the HBB gene, that is located on the number-11 chromosome. This gene contains the instructions for making the beta chains that are part of haemoglobin A (see gure 11.5). The allele of the HBB gene on each of Giovannis number-11 chromosomes is slightly different from that in his sister (see gure 11.5). This slight difference is enough to alter the information encoded in that gene, so that Giovanni cannot make beta chains. In this chapter we will identify this difference and explore how it produces its effect on Giovannis phenotype. Beta thalassaemia is not uncommon among Australians whose parents came here from southern European countries. In the box opposite, you can read the personal story of Soltirios, a man with beta thalassaemia.
11 11 Giovanni Genotype tt
11 11 Maria Genotype TT
Figure 11.5 The HBB gene

is located on the number-11 chromosome. Genotypes of Giovanni and Maria are shown. What must their parents genotypes be?
386
PERSONAL STORY
Soltirios living with thalassaemia
I was born in Melbourne, to Greek Australian parents. Part of my heritage included thalassaemia. Although it was not diagnosed at the time of my birth, my mother had heard of thalassaemia in Greece. Later, when I was appearing rather ill and anaemic as a four year old, it was diagnosed at the hospital. An illness that made me feel very tired as a child, unable to walk long distances or to play with the energy of other children soon provided other nightmares as part of the treatment. Around ve years old, I began having regular blood transfusions at hospital. These varied from fortnightly to eight weekly. My haemoglobin level was around six before I began transfusions. After I was initiated into the transfusion regime, doctors aimed to maintain my haemoglobin level at or above nine prior to a transfusion. Due to the lack of volume of blood in my body and the weak development of my veins, transfusions were particularly traumatic for me as a child. The painful search for a suitable vein to put the drip into and the stays in hospital became part of the experience of living with thalassaemia. system was further compromised and penicillin was prescribed. To this day, however, I have not suffered a major infection other than the regular cold. Regular transfusions now provided another challenge. The extra iron left from all those blood transfusions could not be removed by my body and was beginning to store itself in my vital organs. An ironchelating agent, Desferal (desferrioxamine), was prescribed to be administered as a single intra-muscular injection daily. This became another painful daily reminder of thalassaemia. The Royal District Nurse would come to my school on weekdays and I would be called to have the injection. Other children saw this and it added to their curiosity. I did not reveal to them what I had to live with. During my early teen years the Desferal injection was replaced by a more effective administration regime. Using a device called a slow-infusion pump, I now administered the Desferal injection myself. The pump administered the injection over a ten-hour period (overnight). Of course, as a teenager, this meant a severely curtailed nightlife at home. I did not want to have this thing strapped to me while going out. I didnt want people to see me as different or pity me, and I did not want to deal with their questions, no matter how well intentioned. Diet was not a real issue for me apart from abstaining from high-iron foods like lentils, which I did not care too much for. As long as I kept up with regular blood transfusions and using my pump, I could lead a very normal life. But using the pump is painful physically and a hassle socially. If I was not vigilant in its use I was warned that other complications could arise such as heart and liver problems, diabetes and eventually death. Ironically, the transfusions would kill me. Its a life-long condition but one that is not impossible to deal with. Excellent support at hospital by people that I now have known for over 25 years means I have an extended family to support me. Plans for the future need to be realistic. In nding a life partner I have to be conscious of the possibility that thalassaemia could be passed on to my children and its severity depends on my partners carrier status. Over 30 years ago, my parents were rst confronted with thalassaemia in a language and environment that was very difcult. They suffered as much or more than I have. I was asked once whether I regret having being born with this condition. I sincerely say that I would live through it all again because I have learned so much and it has made me a stronger-willed person.
Figure 11.6 Soltirios

Around seven years old, I had my spleen removed as it was using too much of my valuable red cells (it was trying to do its job of removing the sick thalassaemic red cells and had become bloated with its desperate drive to destroy them). Without a spleen my immune
387
KEY IDEAS
Various kinds of haemoglobin are found in red blood cells. Each kind of haemoglobin consists of four protein chains each with an iron-containing haem molecule. The gene that controls the production of the beta chains of haemoglobin A is the HBB gene on the number-11 chromosome. Absence of beta chains is an inherited disorder known as beta thalassaemia.
QUICK-CHECK
1 What kinds of haemoglobins are normally found in the red blood cells of people after birth? 2 What kinds of protein chains make up haemoglobin A? 3 What role does Desferal play in the treatment of thalassaemia?
Genes in action
Genes are made of DNA that contains information in coded form. When genes are active, these instructions are decoded and are expressed in the phenotype. In eukaryote organisms, the instructions present in genes are decoded in the cytoplasm of the cell. But, a problem exists. The genes are located in the DNA of the chromosomes that are locked away in the nucleus of the cell (see gure 11.7). How do genetic instructions get from the nucleus to the cytoplasm? When a gene becomes active, it rst makes a mobile copy of the coded instruction that it contains. This occurs by a process known as transcription. This mobile copy of a genetic instruction can leave the nucleus and move to the cytoplasm where the instruction is decoded. This occurs by a process known as translation. So, gene action involves two processes: transcription and translation.
Figure 11.7 The nucleus is where

DNA is located and where the process of gene transcription occurs. The cytoplasm is the site where the process of translation occurs.
388
ODD FACT
Three kinds of RNA occur in cells: messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA). By far the most common is rRNA since it forms part of every ribosome, a cell organelle that is present in large numbers in the cell cytoplasm. rRNA is also found in the nucleolus.
Transcription: copying the original

The nucleus of a eukaryote cell is like a safe that contains the genetic masterplan in the form of DNA. The genetic masterplan containing the entire set of instructions for an organism is like the complete plan for the construction of a complex structure, such as a jumbo jet. One gene or instruction for a particular protein is like the plan for making one component of the jet, such as a wing ap. The workers at the site where the wing aps are made do not work directly from the complete masterplan; instead, they have copies of the relevant part. Likewise, before a genetic instruction in DNA is decoded, that instruction is copied (transcribed) from the genetic masterplan which remains in the nucleus. This copy is encoded in a different nucleic acid called ribonucleic acid (RNA). Because the role of this particular RNA is to carry a copy of a genetic instruction from the nucleus to the cytoplasm, it is known as messenger RNA (mRNA).
DNA and RNA compared

DNA and RNA are both nucleic acids, but they differ in several ways (see table 11.2).
Table 11.2 Summary of differences

between DNA and RNA
Feature sugar in nucleotide sub-unit bases in nucleotide sub-unit usual structure
DNA deoxyribose A, G, C and T double-stranded chain forming a double helix ribose
RNA
A, G, C and U single-stranded chain
Figure 11.8 shows the structures of DNA and RNA. The sugar in DNA (shown by the pink symbol) is deoxyribose, while the sugar in RNA (shown by the brown symbol) is ribose. Three of the nucleotide bases, A G and C, are present in both DNA and RNA, but T (thymine) is found in DNA only and U (uracil) is found in RNA only. Note that DNA consists of two chains while RNA consists of a single chain only.
(a) (b)
5' P A P G P T P

C
Figure 11.8 (a) Representation of

part of a DNA double helix. Note that the backbone of each chain is made of sugar joined to phosphate. Two chains run in opposite directions. The four bases found in DNA are A = adenine, G = guanine, T = thymine and C = cytosine. What holds the two chains together? (b) Representation of part of an RNA chain. Like DNA, it also has a sugarphosphate backbone. The four bases present in RNA are A, G, C and U = uracil.
5' 3' T P
P A P G
P A P G P
P U P C 3'
C 3'
DNA
5'
RNA
Pairing or hybridisation can occur between the bases in one DNA strand and complementary bases in an RNA strand as follows: A in DNA pairs with U in RNA T pairs with A C pairs with G G pairs with C.
389
DNA template
C
G
RNA
This pairing means that a DNA chain can act as a template to guide the construction of RNA with a complementary base sequence (see gure 11.9). This means that the genetic information in DNA can be accurately copied into RNA during the process of transcription. Consider a DNA template with the base sequence DNA template . . . ATGCCTGAAT . . . This DNA can act as a template to guide the formation of a RNA molecule with the complementary base sequence as follows: mRNA transcript (copy) . . . UACGGACUUA . . .
Figure 11.9 Because of pairing

of complementary bases in DNA and RNA, one DNA chain can act as a template to build an RNA chain with a predictable nucleotide sequence. What does an A in DNA put in place in RNA?
From DNA to mRNA: step by step

A particular gene in the nucleus is switched on at a speci c stage of development. In the case of the HBB gene, this gene becomes active during late fetal development in certain bone marrow cells. Transcription takes place in a series of steps (see gure 11.10). 1. An enzyme, known as RNA polymerase, attaches to a region of DNA in the upstream region of the template strand. The double-stranded DNA of the gene unwinds and exposes the bases of the template strand. 2. The base sequence of the DNA template guides the building of a complementary copy of the mRNA sequence. The RNA polymerase enzyme moves along the DNA template and, as it moves, complementary nucleotides are brought into place and, one by one, are joined to form an RNA chain. 3. The result of this process is a single-stranded molecule, called pre-messenger RNA. The base sequence in the pre-mRNA molecule is complementary to the base sequence of the DNA of the template strand.
Figure 11.10 Transcription occurs

in the cell nucleus. The enzyme, RNA polymerase, moves along the DNA template building an mRNA molecule at the rate of about 30 bases per second. How long would it take to build an mRNA molecule that is 10 000 bases long?
DNA A T G G C T T A G A A
Free ribonucleotides A G U G C U G U A U A C G U C A A T A AA TT T A C G RNA polymerase
G C
A G A mRNA
fa t
Pre-mRNA is modi ed after transcription

The primary product of translation is pre-mRNA, also known as the primary transcript. The sequence of bases in the pre-mRNA is complementary to all the DNA bases of a gene, both introns and exons (refer back to chapter 10, pages 373 and 375 6). The pre-mRNA is altered after it has been transcribed (see gure 11.11), a process known as post-transcription modi cation.
1 Intron Exon Exon Intron Exon Pre-mRNA Discarded introns mRNA 3 AAAAAAA Final mRNA
Splicing of pre-mRNA is carried out by a complex known as the splicosome. This complex consists of protein and RNA.
Figure 11.11 Post-transcription modi cation of pre-mRNA. In step 3, the denotes the cap and AAAAA...AA denotes the poly-A tail.
What happens is that the regions of the pre-mRNA that correspond to the introns in the coding region of the gene are cut out, producing a shorter mRNA
390
Natureofbiologybook2
molecule. The HBB gene has two introns and, as a result, two sections are cut from the pre-mRNA. The nal mRNA molecule is chemically capped and a poly-A tail is added to produce the operational mRNA that will move across the nuclear membrane into the cytoplasm carrying with it a copy of the information from the DNA template. In the next section, we will examine how the genetic information that is copied into mRNA is decoded (translated) into a particular protein chain.
KEY IDEAS
Coded genetic instructions are located in the DNA of the nucleus of eukaryote organisms. DNA and RNA are both nucleic acids, but differ in several ways. During transcription, the information in the template strand of the DNA of a gene is copied into a RNA molecule. The base sequence in a single strand of DNA acts as a template to guide formation of pre-mRNA. The nal mRNA molecule results when regions corresponding to introns are removed.
QUICK-CHECK
4 Where does transcription occur? What is the end product of this process? 5 A template strand of DNA includes the base sequence: TATCGGCAT Write the base sequence of the complementary template. 6 A strand of mRNA includes the base sequence: AUGUAUCCG Write the base sequence of the DNA template. 7 List two ways in which RNA differs from DNA. 8 List two differences between pre-mRNA and mRNA.
Translation: decoding genetic instructions

The decoding of the genetic instructions occurs through the process of translation which takes place in the cytoplasm. By the end of this process, the genetic instructions carried in mRNA have been decoded and translated into a protein chain built of amino acids. The coded instruction in the mRNA is not changed in this process, just as the plan of a jumbo jet part is unaltered after the part is made. Translation involves the combined action of several agents (see table 11.3). The mRNA moves from the nucleus to the cytoplasm where it attaches to sub-microscopic organelles known as ribosomes (see gure 11.12).
Figure 11.12 Ribosomes are composed mainly of a type of ribonucleic acid, known
as ribosomal RNA (rRNA). In this electron photomicrograph, ribosomes appear as dark dots located on the endoplasmic reticulum.
391
Table 11.3 Players and places in translation (Many enzymes are also involved.)
Agents DNA in the nucleus mRNA ribosomes tRNA amino acids protein chain Analogy masterplan with complete set of instructions working copy of one instruction construction site carriers of raw material raw material end product
(a)
Amino acid
TRANSFER RNA
Anticodoncodon base pairing
Messenger RNA
The construction of a protein according to the coded instructions in mRNA involves the assembly of amino acid sub-units. The various amino acids are present in solution in the cytosol. How are the correct amino acids selected from this solution? (b) Each amino acid is brought to the mRNA on the ribosomes by a carrier molecule called AA C A transfer RNA (tRNA). Each tRNA molecule consists of a single strand of 76 nucleotides coiled and paired with themselves. At one end A of each tRNA molecule are three bases that a a make up an anti-codon. At the other end of CU U G a tRNA molecule is a region which attaches to one specic amino acid (see gure 11.13). An enzyme, amino acyl tRNA synthetase, catalyses the linking of each amino acid to its specic tRNA carrier.
Codon
From mRNA to protein: step by step

The information in mRNA is present in coded form as sets of three bases or triplets. These triplets, such as AGG and UCU, are called codons. Most codons contain the information to add one specic amino acid to a protein chain. In addition, one codon (AUG) is a START TRANSLATION instruction, and three different codons (UAA, UAG and UGA) are STOP TRANSLATION instructions (see table 11.4). The instructions in a mRNA molecule are decoded three bases (or one codon) at a time. Translation begins at the start adding amino acids signal (AUG codon) (see gure 11.14a). This codon both starts the process of building a protein chain and puts the amino acid, met, into place as the rst amino acid in the chain. Then, the next three bases are translated by adding the next amino acid to the growing protein, and so on (see gure 11.14b). As each codon is translated, the tRNA molecule with the complementary anticodon pairs momentarily with the mRNA. The pairing between bases in codons and the complementary bases in an anti-codon is as follows: A pairs with U U pairs with A C pairs with G G pairs with C. So, when the mRNA codon UUU is reached, the tRNA carrier molecule that has the anti-codon AAA comes into place with its specic cargo of the amino acid, phe. The amino acid carried by that tRNA is brought into the correct position to be joined into the growing protein chain. Amino acids continue to be added until a STOP signal is reached which stops the addition of amino acids to the protein chain.
Figure 11.13 (a) Transfer RNA

(tRNA) molecule. At one end is an amino acid attachment site and, at the opposite end, an anti-codon region. How many bases make up an anti-codon? (b) A simpler representation as used in this textbook
In this text, the term protein chain is used to refer to a single chain built of amino acid subunits. Polypeptide is another term for a chain consisting of amino acids.
392
Table 11.4 Genetic code shown as the 64 mRNA codons and information they specify.
(See appendix for the full names of the amino acids.) The codon AUG is a start signal and it also codes for the amino acid, met. Note the three stop signals. The genetic code in mRNA codons is complementary to that in DNA. The genetic code in DNA is shown in the appendix.
The colour coding in table 11.4 groups amino acids according to their side chains; for example, those with a positive charge are shown in blue.
mRNA codon UUU UUC UUA UUG CUU
Amino acid phe
mRNA codon UCU UCC
Amino acid
mRNA codon UAU
Amino acid tyr
mRNA codon UGU
Amino acid cys
UAC ser UAA STOP UAG CAU his CAC pro CAA gln CAG AAU asn AAC thr AAA lys AAG GAU asp GAC ala GAA glu GAG
UGC UGA UGG CGU CGC arg CGA CGG AGU ser AGC AGA arg AGG GGU GGC gly GGA GGG STOP trp
UCA UCG CCU leu CCC CCA CCG ACU ile ACC ACA START /met ACG GCU GCC val GCA GCG
CUC CUA CUG AUU
ODD FACT
Messenger RNA (mRNA) formed during gene transcription has a short life. This is in contrast to ribosomal RNA (rRNA), which forms part of the ribosomes, which is very stable.
AUC AUA AUG GUU GUC GUA GUG
What is the mRNA codon for STOP? Will this have a corresponding anticodon on a tRNA carrying an amino acid?
(a)
mRNA AUG
UA
RIBOSOME
aa
Figure 11.14 (a) The mRNA

molecule attaches to a ribosome. In turn, as the ribosome moves along the mRNA molecule, each codon pairs with the tRNA with the complementary anti-codon. (b) The amino acids carried by each tRNA molecule are joined to form a chain. The nal product is a protein consisting of a chain of amino acid sub-units, also termed a polypeptide.
(b) mRNA GGGCUGCAA C C C GA C
GU U
aa
aa
aa
aa
aa
aa
aa
393
Putting it all together: transcription and translation

The production of a particular protein, such as beta chains of haemoglobin, starts in the cell nucleus. It is here that pre-mRNA molecules are produced by transcription from a template DNA chain. The mRNA leaves the nucleus and moves to the cytosol where it becomes attached to ribosomes. It is here that protein chains are formed by translation of mRNA. Figure 11.15 shows a summary of the processes of transcription and of translation. For simplicity, this diagram omits one important step. Can you identify the missing step? By referring to the genetic code shown in table 11.4 (see page 393), identify the amino acid that is about to be added to the growing protein chain in this diagram.
Transcription Polypeptide chain Polymerase Amino acid mRNA Nucleus

C A U Translation CG UG G A G U U C C A G C G U A G GC CA U
tRNA
A C C U A C
UG G A
Codon
A
A C C U AC UG A
Figure 11.15 Representation

of the processes of transcription and translation in a eukaryote cell (Source: National Human Genome Research Institute). Which of these processes involves the action of three different kinds of RNA?
Ribosome
mRNA
U G A A C A U G C G U GA C
Alternative splicing of pre-mRNA

ODD FACT
One scientist has suggested that each gene is like a Swiss army knife: it can do several jobs, depending on how it is handled (or, in the case of a gene, how it is regulated).
The human genome contains only 20 000 to 25 000 genes and this range is typical of other mammals. In the past, it was accepted that one gene had a single function as, for example, producing one particular protein this is the one gene one polypeptide concept. The question remains: How can a relatively small number of genes produce the complexity of structure and function of a living mammal? Research is now revealing that one gene can be regulated in different ways so that it can produce more than one protein. This means that: one gene could produce one protein at one stage of development but a different protein at another stage of development one gene could produce a particular protein in one tissue but a different protein in another tissue. It is estimated that about 30 per cent of human genes are regulated to operate in this way. The complexity of mammals is not in the number of genes that they have, but in the processes by which their genes are regulated.
394
How might one gene produce different protein products at different developmental stages and in different tissues? One way is through alternative splicing of the pre-mRNA molecules from a single gene. For example: intron retention can produce different mRNA molecules from the same premRNA, depending on whether or not all the introns are cut out and discarded (see gure 11.16a) juggling exons can produce different mRNA molecules from the same premRNA, depending on whether or not all the exons are used in the nal mRNA (see gure 11.16b).
(a) INTRON RETENTION Intron Intron Exon
Figure 11.16 Alternative splicing

involving either introns or exons (a) Different mRNAs produced by intron retention (b) Different mRNAs produced by juggling exons. In both cases, are other mRNAs possible?
Exon
Exon
(b) EXON JUGGLING Intron Exon Exon Intron Exon
Alternative splicing means that the number of outputs from the genetic instructions (genes) in a genome is far greater than the number of genes. Identifying how the DNA of one gene can be regulated to produce different products is an exciting area of ongoing research.
Comparing prokaryotes and eukaryotes

The living world can be divided into two groups: the prokaryotes and the eukaryotes. Prokaryotes comprise the unicellular bacteria and the archaeans. The remainder of the living world protists, fungi, plants and animals comprise the eukaryotes, with a few being unicellular, but the majority being multicellular.
Differences in genome organisation

Figure 11.17 shows some typical prokaryotic cells. Note that there is no nucleus such as occurs in eukaryotic cells. Some differences in the organisation of the genetic material in these two groups are outlined in table 11.5.
Gene action: comparing prokaryotes and eukaryotes

Figure 11.17 Modern bacterial
cells. Like the earliest form of life on Earth, these are unicellular organisms separated from their external environment by a cell membrane. Does each have a separate membrane-bound nucleus?
Gene action in prokaryotes and eukaryotes is very similar; both involve transcription of mRNA from a DNA template and translation of protein chains on ribosomes according to the same genetic code. However, there are a few differences in gene action between prokaryotes and eukaryotes: Location of gene action. In eukaryotes, the processes of transcription and translation occur in different cell compartments: transcription of mRNA occurs in the nucleus, while translation of mRNA on ribosomes takes place
395
Table 11.5
Prokaryotic DNA The main chromosome is a circular molecule of DNA, called a plasmid. DNA is naked (see gure 11.17). DNA comprises unique nucleotide sequences. DNA is free within the cell. Coding sequences of genes are uninterrupted. Eukaryotic DNA Each chromosome is a linear molecule of DNA. DNA exists in complexes with proteins called histones (refer back to gure 1.30). DNA contains many repeated nucleotide sequences. DNA is enclosed within the nucleus. Coding sequences (exons) of genes are interrupted by introns.
As well as the main chromosome, Plasmids are absent. additional DNA in the form of plasmids is present.
ODD FACT
Ricin from the castor oil plant breaks down one of the rRNA building blocks of ribosomes in eukaryotes. Why is it such a deadly poison?
in the cytoplasm. In prokaryotes, however, these processes are not separated because there is no nucleus. This means that, in prokaryotes, as fast as mRNA molecules are transcribed, they can bind to ribosomes and translation can begin. mRNA. (1) The mRNA produced in prokaryotic cells lasts just a few minutes, while eukaryotic mRNA survives for hours or days. (2) Post-transcriptional modication of mRNA must occur in eukaryotes but this does not occur in prokaryotes. Why? Ribosomes. The ribosomes in prokaryotes and in eukaryotes are both effective in translating the coded information in mRNA molecules to protein chains, but the ribosomes in the two groups differ in size. This difference is the basis of action of some antibiotics used to treat bacterial infections. Antibiotics, such as tetracycline, interfere with the binding of tRNA molecules to bacterial ribosomes so that the tRNAs cannot deliver the amino acids that they normally transport. As a result, tetracycline inhibits bacterial translation. This makes tetracycline an effective antibiotic. Why? At the same time, this drug does not affect transcription in eukaryotic cells.
KEY IDEAS
Gene translation occurs in the cytoplasm and involves cell organelles known as ribosomes. mRNA instructions are encoded as sets of three non-overlapping bases called codons. Translation commences when a START codon is translated; this codon not only starts translation but also puts the amino acid, met, in place. As each mRNA codon is translated, a specic amino acid is brought into place by the tRNA molecule with the complementary anti-codon. Translation ceases when a STOP codon is reached. The end product of translation is a protein chain or polypeptide. Differences exist between the organisation of the genomes of prokaryotes and of eukaryotes. Gene action in these two groups is essentially similar but with some minor differences.
396
QUICK-CHECK
9 Identify the difference between the members of the following pairs: a codon and anti-codon b mRNA and tRNA c amino acid and protein d START codon and STOP codon. 10 List the anti-codons in tRNA that would be complementary to the following mRNA codons: AAG, GGC, UUU. 11 A tRNA molecule has the anti-codon GAG. a To which mRNA codon would this tRNA temporarily attach? b What amino acid would this tRNA carry? 12 What product typically results from gene translation? 13 Identify one way in which one gene could produce more than one protein product.
Location HBB gene
Gene action in thalassaemia

The HBB gene on the number-11 chromosome controls the production of the beta chains of haemoglobin. This gene contains about 1600 base pairs (bp) (see gure 11.18). How many introns are present in the HBB gene? How many exons? The exons make up the coding region of the gene and the information coded in the exons is translated as a protein chain. Usually, this protein chain is the beta chain found in the major haemoglobin of adult human red blood cells. Maria is homozygous for the normal allele of the HBB gene. In Maria, the coding region of both of her HBB genes is transcribed into mRNA that contains the information for construction of normal beta chains. Each normal beta chain is a protein made of 146 amino acids. Because her beta chains are normal, they can become part of haemoglobin A molecules. In contrast, Giovanni has two copies of an altered allele of the HBB gene and cannot make normal beta chains. His red blood cells contain no haemoglobin A (see gure 11.19).
Number-11 chromosome 1 30 31 104 105 146
Exon
Exon Intron Intron HBB gene
Exon
Figure 11.18 Representation of

the HBB gene from the number-11 chromosome. The numbers denote the amino acids that are coded by the DNA of the gene.
Giovanni
tt
Rate of chain production Gamma Rate of chain production
Red blood cells
Alpha
Maria
TT
Gamma
Beta
Alpha
Figure 11.19 Giovanni and Maria compared. Who is able to make beta chains?
The base sequence of part of the template strand of the HBB gene for Maria is shown in table 11.6. Notice that when the alleles of Marias HBB gene are translated, her red blood cells produce beta chains with the expected 146 amino acids.
397
Table 11.6 Action of the form of HBB gene in Maria

Maria Template strand of DNA. . . . - TGA - CGG - GAC - ACC - CCG - TTC - CAC - TTG - CCA - . . . GTG - ATT When this gene is transcribed, the result is: ... Codons in mRNA 12 13 14 15 16 17 18 19 20 - . . . 146 147
. . . - ACU - GCC - CUG - UGG - GGC - AAG - GUG - AAC - GUG - . . . CAC - UAA
When this gene is translated, the result is: ... Amino acids in protein 12 13 14 15 16 17 18 19 20 . . . 146 - 147
. . . - thr - ala - leu - trp - gly - lys - val - asn - val - . . . his - STOP
There is just a single difference between Giovannis DNA and that of his sister, Maria. His alleles differ at one location in the template strand. The change is a base substitution in which a T has been replaced by an A (see table 11.7). This single change in Giovannis DNA affects the mRNA transcribed by this gene. This change affects the seventeenth codon in the mRNA. Instead of the usual AAG, this codon is UAG in Giovanni. When Giovannis altered seventeenth codon is translated, it gives the instruction: STOP adding amino acids to the protein. Marias normal seventeenth codon is translated as the instruction: Add the amino acid, lys, to the protein chain.
Table 11.7 Action of the form of HBB gene in Giovanni

Giovanni Template strand of DNA . . . - TGA - CGG - GAC - ACC - CCG - ATC - CAC - TTG - CCA - . . . GTG - ATT
When this gene is transcribed, the result is: ... Codons in mRNA 12 13 14 15 16 17 18 19 20 . . . 146 - 147
. . . - ACU - GCC - CUG - UGG - GGC - UAG - GUG - AAC - GUG - . . . CAC - UAA
When this gene is translated, the result is: ... Amino acids in protein 12 13 14 15 16 17
. . . thr ala leu trp gly STOP
ODD FACT
What happens if a DNA mutation like ATC to ATG occurs? This mutation changes a stop code to a code to add an amino acid. As a result, translation continues until the next stop signal is reached. An example of this type of mutation is seen in the HBA gene of some people. The protein chain produced is longer than normal with 172 amino acid sub-units instead of the normal 141.
This change in Giovannis HBB gene has profound consequences. The construction of beta protein chains stops far too early. Instead of having the usual 146 amino acids, the beta chains have only 16 amino acid sub-units. This shortened chain cannot form part of the structure of haemoglobin. So, Giovannis red blood cells do not contain any haemoglobin A. Because Giovanni produces no functional beta chains, he is said to have the form of beta thalassaemia that is called beta-zero (0) form. Giovannis parents do not have beta thalassaemia. They are both heterozygous for this gene with one normal allele and one altered allele. Beta thalassaemia is a recessive condition and the presence of one normal allele masks the presence of the altered allele. However, the egg cell and the sperm cell that fused to form the zygote that developed into Giovanni each carried one copy of the altered allele. Can you draw a Punnett square to show the cross of Mr and Mrs C? What is the expected outcome?
398
Beta-plus thalassaemia
Another form of beta thalassaemia, known as the beta-plus (+) form, exists. In this form, beta chains are produced, but their rate of production is very much lower than normal. As a result, people with beta-plus thalassaemia show some of the symptoms of thalassaemia, but the symptoms are less serious. The box below explains how beta-plus thalassaemia arises.
BETA PLUS ANOTHER FORM OF THALASSAEMIA

Tran is unrelated to Giovanni. He has beta thalassaemia, but does not show the same severe symptoms seen in Giovanni. Trans red blood cells contain normal haemoglobin A, with the expected two alpha and two beta chains. However, the relative amount of haemoglobin A is much lower than normal. This form of thalassaemia is called beta-plus thalassaemia to distinguish it from the more severe beta-zero form. In people with beta-plus thalassaemia, the coding region of the DNA of the HBB gene is normal. But the gene functions in slow gear. The defect in Tran is in the DNA upstream of the coding region of the HBB gene. A single base substitution in the DNA at a position 29 bases upstream from the start of the coding region has affected the TATA promoter region. This alteration affects the process of transcription, so that the amount of mRNA produced is reduced to about 25 per cent of normal. This reduction in the amount of mRNA copies of the genetic instruction then results in a lowered rate of translation of this instruction into beta chains.
How many alleles?

In Mendelian genetics, genes are often identied as having a few, often just two, alleles. This is a simplication because one gene can have a very large number of different forms or alleles. Every alteration of one gene is an allele of that gene. Alterations of a gene can include many kinds of changes, such as: base substitutions base additions (insertions) base deletions and these changes may involve one or more bases. Alterations to a gene can affect its coding sequence or may occur in the anking regions, upstream or downstream. We commonly recognise just two different alleles of a gene in terms of phenotype, such as unaffected or showing a disorder. However, at the level of the DNA of the gene itself, a very large number of alleles can be recognised, each with some alteration in base sequence compared with the base sequence of the unaffected allele.
Many alleles cause beta-zero thalassaemia

We commonly say that the HBB gene has two alleles: T: normal beta chains produced t: normal chains not produced. However, this is highly simplied. In the human population, many forms of the t allele exist, all producing some degree of clinical expression of the symptoms of beta thalassaemia; that is, either an absence or a reduced amount of beta chains. Giovanni has two copies of an altered form of the gene that affected the seventeenth codon in the mRNA produced by the DNA. However, beta-zero
399
thalassaemia can arise from many other changes in the base sequence of the HBB gene. Each of these changes is a different allele of the HBB gene. Tran also has beta thalassaemia. He and his parents came to Australia from Vietnam. A different alteration of the HBB gene exists in Trans family. While both Giovanni and Tran have beta thalassaemia and the same gene is involved, different alleles of this gene are responsible for the condition in each boy.
KEY IDEAS
In beta-zero thalassaemia, no beta protein chains are produced. Beta-zero thalassaemia can result from a single base substitution in the coding sequence of the HBB gene that affects both the mRNA transcribed and the protein made during translation. Many mutations of a gene can occur so that many alleles of one gene can exist.
QUICK-CHECK
14 Do all people with thalassaemia (beta-zero form) have identical genotypes? Explain. 15 If a gene normally codes for a protein with 22 amino acids, what change in the DNA of the gene could result in this protein having only eight amino acids?
All genes produce RNA . . . most then produce protein

All known genes contain coded information. In most genes, the coded information is a set of instructions for joining amino acids to build various proteins. In eukaryotes, messenger RNA (mRNA) is an intermediary in this information ow and it carries the information from DNA to the cytoplasm. The end product of the action of these genes is a protein chain made of amino acids:
Information in DNA Transcription Information in mRNA Translation Amino acid sequence in protein
The information in some genes does not always result in the output of proteins. Some genes produce other kinds of RNA, such as various transfer RNAs (tRNAs) and ribosomal RNAs. tRNAs are the carrier molecules that transport amino acids to ribosomes. rRNAs form part of the structure of ribosomes, the cell organelles where translation occurs. A summary of the action of these genes can be shown as: Information in DNA Information ow Ribosomal RNA (rRNA) is produced in large quantities in the nucleus of eukaryote cells. The rRNA is stored in the nucleus where it forms a structure
400
tRNA and rRNA end products
known as the nucleolus. When rRNA is needed to form part of the structure of ribosomes, it moves from the nucleolus to the cytoplasm. Genes located on the short arms of human chromosome numbers 13, 14, 15, 21 and 22 code for the production of rRNA. The regions on each of these chromosomes where the ribosomal gene loci are located are termed nucleolar organiser regions (NORs). A secondary constriction or narrowing marks the position of the NOR on each chromosome (see gure 11.20a). Because rRNA is produced in very large quantities in a cell, it is not surprising that multiple copies of the gene are carried on several different chromosomes. Figure 11.20b shows some human chromosomes that have hybridised with a red uorescent probe that binds to the ribosomal genes. The probe has bound to the short arms of some chromosomes revealing the location of the ribosomal genes on these chromosomes.
(a) (b)
13
14
15
21
22
Figure 11.20 (a) Human

chromosomes 13, 14, 15, 21 and 22. Note the secondary constriction (arrowed) on the short arm. This forms the nucleolar organiser region (NOR) and is where the ribosomal genes are located. (b) Photomicrograph of human chromosomes hybridised with a probe that is specic for the gene that controls production of ribosomal RNA (rRNA). The rest of the chromosomes are counterstained with a blue dye. Note the multiple locations of this gene.
Genes have various functions

Structural and regulator genes
ODD FACT
In human cells, each nucleolar organiser region (NOR) consists of a segment of DNA more than 3 000 000 base pairs in length. The DNA of each NOR contains about 80 repeats of the ribosomal gene.
Genes vary in the functions that they carry out in the cells of an organism. Some genes produce proteins that become part of the structure and the functioning of the organism. These genes are termed structural genes. Some genes produce proteins that control the action of other genes. These genes are termed regulator genes and their actions determine whether other genes are active (on) or not (off) and, if active, the rate at which their products are made. Genes switch other genes on or off by producing proteins that act in one of two different ways: 1. Some proteins, known as DNA-binding proteins, bind to regions of nuclear DNA near genes and directly switch these genes on or off.
401
2. Some proteins bind to receptors on the membrane of cells in their target tissue and trigger a series of intercellular reactions that switch genes on or off; these are signalling proteins. Genes that control embryonic development in insects and in vertebrates have been discovered. These master genes, known as homeotic genes, are examples of regulator genes and they play an important role in embryonic development. They control the action of hundreds of other genes that are needed to build the various parts of an animal body in their correct locations. In insects, for example, when a particular homeotic gene malfunctions, the result is an insect that has, instead of antennae, legs on its head (see gure 11.21). If another homeotic gene does not operate normally, the affected insect may have an antenna where it would normally have a wing. This observation provides evidence that some genes control the orderly events that occur during embryonic development.
(a) Halteres (b) Wings replace halteres
Antennae
Legs replace antennae
Figure 11.21
Mutations in master or homeotic genes result in the appearance of body parts in unexpected locations. (a) Normal y (b) Fly has mutations in homeotic genes that result in the appearance of a second pair of wings instead of halteres and legs instead of antennae.
Like insects, mammals also have homeotic genes, known as HOX genes. These genes play key roles during embryonic development in organising the mammalian body plan that includes a brain at the anterior, a series of paired blocks on each side of the developing vertebral column (spine), forelimbs on the anterior regions, hindlimbs at the posterior region and ribs on some vertebrae but not on others. In mammals, the HOX genes are arranged in four gene clusters on four different chromosomes, with each cluster of genes being arranged in tandem (one after the other). In humans, the four groups of homeotic genes are: the HOXA complex of 11 genes on chromosome 7 the HOXB complex of 10 genes on chromosome 17 the HOXC complex of 9 genes on chromosome 12 the HOXD complex of 9 genes on chromosome 2. Mutations in homeotic genes reveal how they control the pattern of the body plan during embryonic development. For example, in mice, mutation of the HOXC8 gene results in an extra pair of ribs. In humans, mutation of the HOXD13 gene results in limb abnormalities, with an extra digit between the third and fourth digits and with all three digits fused. If the genes at one end of the HOXD complex are removed by a chromosomal deletion, severe limb and genital deformities result. Homeotic genes produce DNA-binding proteins. By binding to the DNA near other target genes, these proteins can switch these genes on and off. The DNAbinding proteins produced by homeotic genes carry a net positive charge (owing to the presence of amino acids, such as arg and lys) that enables them to bind to DNA that carries a negative charge (see gure 11.22).
Figure 11.22 Homeotic genes produce a polypeptide with a region that carries + +
charges that can bind to DNA. Here, the DNA-binding region of the polypeptide is shown bound to DNA (purple).
402
ODD FACT
High doses of vitamin A (retinoic acid) appear to affect the action of some of the HOX genes, resulting in major malformations in developing embryos involving heart, limbs, central nervous system and facial bones.
Would you expect homeotic genes to occur in plants? What possible explanation might be given for a plant that has an extra ring of stamens in place of petals?
KEY IDEAS
All active genes produce RNAs of some kind. Most genes transcribe mRNAs that are then translated into proteins. Some genes produce other kinds of RNA, such as tRNA and rRNA, and these are the end products. Genes can be classied in various ways.
QUICK-CHECK
16 List one difference between a structural gene and a regulator gene. 17 What is a homeotic gene?
Self-replication: copying itself

DNA is a remarkable molecule. We have already seen that it is an informationcarrying molecule that contains coded information for building the large number of different kinds of proteins that are present in an organism. DNA is like a genetic instruction manual. However, it is an instruction manual with a difference. DNA molecules come with an inbuilt photocopier because they can direct their own exact copying. So, a second remarkable feature of DNA is that it is self-replicating. DNA can control its own replication and make exact copies of itself, over and over. The process by which this occurs is called DNA replication. As a result of this process, the entire genetic masterplan is copied.
Time and place of DNA replication

DNA replication must occur before mitosis takes place in tissues such as the germinal layer of the skin, the digestive tract and the bone marrow. DNA replication is essential for the growth of a baby from a single-celled zygote to a multi-celled individual. Can you think of other body cells in which DNA replication is occurring right now? Figure 11.23 shows plant tissue with some cells undergoing replication. DNA replication also occurs in cells of the gonads during early meiosis prior to gamete production.
Process of DNA replication

DNA replication begins when a region of double-stranded DNA unwinds to form a region of single-stranded DNA (see gure 11.24). Each of the single strands acts as a template for building a new complementary strand. Nucleotide building blocks are the raw material for the process of DNA replication. The nucleotides come into place where there is a G in the template strand, a C-containing nucleotide is brought into place. Where there is a T in the template strand, an A-containing nucleotide is brought into place, and so on. In this way, the base sequence of a double-stranded molecule of DNA controls the order of the nucleotides in two new single strands of DNA. This
403
Figure 11.23 DNA replication

occurs during interphase before chromosomes become visible. This is the S phase of the cycle. Cells in which DNA replication is probably occurring are cells in which the nucleus appears as a denite circular outline. (The one or more small darker regions within each nucleus are nucleoli.)
GC GC
AT T A
CG AT GC T A AT
G A CG AT
T T
Old Old
T A
C
TA GC GC AT
TA CG AT GC GC AT CG TA
CG TA
T A CG
New
AT GC
New
TA CG AT GC
process is catalysed by the enzyme, DNA polymerase. Each nucleotide joins to its neighbour in the chain by a strong sugar-phosphate bond. DNA replication results in the formation of two double-stranded molecules of DNA, each of which is identical to the original double-stranded DNA molecule. The two DNA molecules that are produced contain one old strand from the original molecule and one new newly synthesised strand.
Which model of DNA replication?

The representation in gure 11.24 of DNA replication shows that one DNA molecule replicates to give two new DNA molecules where each has one original chain and one new chain (see gure 11.25a). This is the so-called semiconservative model of DNA replication. Among other possibilities is a conservative model, where the two new DNA molecules consist of one with the two original chains and the other with two new chains (see gure 11.25b). How do we know which model is correct?
(a)
DNA of original cell DNA after one replication DNA after two replication cycles Conservative model Semi-conservative model
Arrows denote direction of synthesis.
Figure 11.24 DNA replication

begins by part of a DNA double helix unwinding. This unwinding is controlled by an enzyme. Complementary strands are built using the old strands as templates. A similar process is involved when DNA re-pairs itself.
(b)
Figure 11.25 Two models of

DNA replication. Which is correct? (a) Conservative model (b) Semiconservative model
404
A CLOSER LOOK AT DNA REPLICATION

DNA replication is a complex process involving the action of many different enzymes. Lets consider a single chromosome, such as the human chromosome 21 that has about 47 million base pairs. 1. The rst step is the unfolding and unwinding of the DNA double helix at hundreds of points, known as replication origins, along the chromosome. Lets now look at what happens at one end of just one of those replication points. 2. The enzyme helicase separates the two DNA strands, separating them like opening a zipper, with the point of opening being termed the replication fork. 3. Where the DNA strands are separated, a short length of RNA binds to each DNA strand under the control of the enzyme, DNA primase. This RNA is needed because the enzyme that builds the new DNA can add nucleotides only to an existing strand and so this RNA acts as a primer (see gure 11.26a). 4. A DNA polymerase enzyme can then proceed to build new DNA strands using each of the old strands as a template (see gure 11.26b). In eukaryotes, the rate of building is about 50 nucleotides per second. (In prokaryotes, DNA replication proceeds at about 1000 nucleotides per second.) Replication of DNA can occur only in the 5 to 3 direction. This is no problem with the so-called leading strand because its new complementary strand can be built continuously in the 5 to 3 direction. The other strand, known as the lagging strand, can be built only backwards and in short discontinuous pieces (see gure 11.26b). When nished, the RNA primers are removed, the gaps are lled by another DNA polymerase and the pieces are joined by the enzyme, DNA ligase. DNA replication is a remarkably accurate process, but errors can occur. Cells also have a mechanism to correct mistakes that occur during DNA replication a bit like having a built-in spell-checker! If, however, a mistake in DNA replication is not corrected, the information encoded in the DNA is changed and this may result in a spontaneous mutation.
(a) Leading strand of DNA 3 RNA primer RNA primer 5 Lagging strand of DNA (b) 3 3 2nd 5 3 Direction of movement of replication fork Replication fork 5 3
3 5
New strands 1st 3 5
Figure 11.26 Outline of DNA replication (a) The two DNA

strands are separated and RNA primers are attached. The DNA will continue to open out in the direction of the replication fork. (b) DNA polymerase adds new nucleotides to the leading and the lagging template strands, in both cases, in the 5 to 3 direction. On the lagging strand, each new piece is added behind the previous piece.
Some mutations in cells cause replication without control, and cancer develops. Some cells fail to die by the process of apoptosis (see pages 345) when they should, because of other mutations. New and more effective treatments against cancers may be possible by applying principles that operate in apoptosis.
This mystery of the model of DNA replication was solved in 1958 by Matthew Meselsohn and Franklin Stahl at the California Institute of Technology. How? 1. Meselsohn and Stahl took bacterial cells and allowed them to multiply for several generations in a growth medium containing heavy nitrogen (N-15) only, so that all nitrogen atoms in these bacterial DNA were heavy nitrogen. 2. These bacterial cells were then transferred to a new growth medium containing only normal light nitrogen (N-14). 3. After one generation (20 minutes), a sample of the new bacterial cells was collected. Any new DNA made by this new generation could incorporate only N-14 atoms. 4. The DNA was extracted from the rst generation bacterial cells. The relative weight of the DNA was determined using a technique that involves centrifugation in a density gradient the lower down the tube, the heavier the DNA. Figure 11.26 shows the expected result with the two different models of DNA replication. Only one of these can be correct. What result did Meselsohn and Stahl obtain? They obtained a single band with their rst generation bacteria (as shown in the middle panel of gure 11.27). So, their experimental results conrmed that newly replicated DNA contained one original and one new chain. This meant that DNA replication was semi-conservative.
405
SEMI-CONSERVATIVE DNA with N-14 only DNA with N-15 only N-14/N-15 L/H
CONSERVATIVE
L/L
N-14 L/L N-15 H/H Pattern expected after one generation
H/H
Figure 11.27 Expected outcomes

for two alternative models of DNA replication where bacterial cells were grown in heavy nitrogen (N-15) and then had their DNA replicated in the presence of light nitrogen (N-14) only. (H = heavy and L = light.)
Control DNA samples
Pattern expected after one generation
KEY IDEAS
DNA molecules can undergo self-replication. DNA replication requires an existing DNA molecule to act as a template for the manufacture of new complementary strands. Nucleotides are the raw materials from which the new strands are constructed. Several enzymes are involved in the process of DNA replication. DNA replication occurs during interphase in body cells that can reproduce by mitosis, and during meiosis in germline cells in the gonads as part of gamete formation.
QUICK-CHECK
18 List two signicant features of DNA molecules. 19 Briey explain the role of the following in the process of DNA replication: a nucleotides b DNA polymerase c template DNA.
Time and place for everything

When are genes active?
Genes vary in the time of their action. Some genes are active in making mRNA and proteins only during a short period of the life span of a person, while other genes are active throughout a persons life. The HBZ gene on the number-11 chromosome controls production of one kind of chain found in a type of haemoglobin that occurs only in mammalian embryos. After the rst few weeks of embryonic development, this gene is switched off and remains silent during fetal development and after birth. A baby boy with the genotype d (Y) for the DMD gene on the X chromosome is healthy at birth and for several years after birth. However, the signs of Duchenne muscular dystropy gradually appear during childhood, so that by about 10 years old, he is conned to a wheelchair (refer back to gure 9.33).
406
Some genes are not expressed on the phenotype until a person is well into adulthood. A person with the genotype Hh has the allele for Huntington disease on the number-4 chromosome. The H allele remains inactive often until middle age when the person shows the rst signs of this devastating disease. The AD1 gene, on the number-21 chromosome, is involved in a familial form of Alzheimer disease. The expression of the specic allele (A) typically occurs after the onset of middle age when the person shows the rst signs of familial Alzheimer disease. Many genes remain active throughout the life of a person. These genes include the genes responsible for controlling the production of enzymes that are essential for cellular respiration, such as the SDH gene located on the number-1 chromosome. This gene controls production of a sub-unit of one of the enzymes (succinic dehydrogenase) essential for cellular respiration.
Where are genes active?

Some genes are active only in the cells of specic tissues: The HBB gene on the number-11 chromosome that controls the production of the beta chains of haemoglobin is active only in those cells of the bone marrow destined to become red blood cells. The DMD gene on the X chromosome that controls production of the protein, dystrophin, is active only in skeletal muscle tissue. The GH gene on the number-17 chromosome that controls production of growth hormone is active only in the pituitary gland at the base of the brain. In contrast, genes involved in controlling production of enzymes involved in cellular respiration are active in all living cells. The phrase gene action refers to the processes of gene transcription and gene translation. The end products of gene action typically are proteins, such as beta protein chains of the HBB gene or amylase enzyme of the AMY gene. However, the nal phenotype of an organism is more complex than just proteins produced by the genes. The box below describes how the action of a certain allele of a gene produces the wrinkled pea phenotype.
GENE ACTION IN MENDELS PEAS

We have seen how the thalassaemia phenotype can arise. What about Mendels peas? The inherited traits in the peas that were investigated by Mendel included the round and the wrinkled pea shapes (see gure 10.4, page 341). Round pea shape (R) is dominant to wrinkled shape (r), so that pea plants with the genotypes RR and Rr produce round seeds, while pea plants with the genotype rr produce wrinkled seeds. Round seeds have a high starch content produced by the action of several starch-making enzymes, including the enzyme, starch-branching enzyme (SBE), which catalyse the conversion of sugars into starches. In contrast, wrinkled seeds lack SBE, and so have a higher sugar content. This higher sugar content leads to a greater accumulation of water in the seed, causing it to swell. When the seed later dries out, it shrinks and produces the characteristic wrinkled phenotype. The gene that carries the coded information for the protein, SBE, has been isolated and analysed. In homozygous RR plants with the round seed phenotype, the responsible gene is a segment of DNA 3300 bp in length; this length includes both exons and introns. In comparison, the DNA of the same gene in homozygous wrinkled rr plants has a length of 4100 bp. So, the presence of a DNA fragment 800 bp long in the normal R allele is the cause of the mutant r allele (table 11.8). Mendels wrinkled peas arose from a gene mutation that was due to an insertion of a long segment of DNA into an existing gene. How does this compare with the change in the gene that was inherited by Giovanni?
Table 11.8 Comparison of round and wrinkled peas, Nature,

vol. 343, 1990, pp. 2089
Round phenotype DNA of gene mRNA protein 3300 bp normal normal; able to act as enzyme (SBE)
Wrinkled phenotype 4100 bp longer longer; unable to act as enzyme
407
Identifying active genes

Of the 20 000 or so genes in a human cell, only some genes are expressed or switched on at a given time. A switched on gene is one that is transcribing the mRNA, while a switched off gene is one that is not producing mRNA. But which genes are active? The pattern of gene activity or gene expression differs between: cells of different tissues cells of the same tissue but at different stages of development normal and abnormal cells, such as cancerous cells cells under different environmental conditions, such as cells exposed to chemical pollutants or drugs. In the past, it was possible to examine whether one or a few genes were active or not. Through a new technology involving microarrays (also known as DNA arrays and gene chips), it is now possible to study large numbers of genes simultaneously or even the entire genome. This means that it is now possible to: identify which genes are active and which genes are switched off compare gene expression in different cell types compare active genes in the same cells under different conditions. A microarray consists of a glass slide (or other solid surface) on which thousands of tiny spots of different DNA molecules are present. Each spot is in a precise location and consists of a tiny amount of single-stranded DNA corresponding to part of one particular gene. Each spot can act as a probe for a particular gene (see gure 11.28). The spots are put in place using a robotic instrument to ensure their precise locations. Typically, the DNA spots in a microarray are organised into segments, with each having X columns and Y rows.
ODD FACT
Commercially available microarrays include one with 32 996 spots covering the mouse genome and one with 32 878 spots covering the human genome. In both cases, each spot comprises a segment of DNA, 60 bases long, from one specic gene.
Figure 11.28 Diagram showing

a microarray (at left), one segment from this microarray (middle) and one spot from a segment (at right). Note that the DNA in each spot contains single-stranded DNA from one specic gene. The DNA spots are typically 150 to 200 micrometres (m) in diameter and the centres of the spots might be 300 m (0.3 mm) apart. So, one segment with 20 rows and 20 columns would t in a square with a side of 6 millimetres.
A G G A C G T
DNA bases
Microarray (chip)
Segment of a chip
Spot containing copies of a single DNA molecule
Part of one DNA strand
Figure 11.29 shows a scientist holding a microarray. Notice also the image of one segment of a microarray on her computer screen.
Applications of microarray technology

The ability to recognise which genes are active can assist our understanding of the role of genes in various diseases. For example, Swedish researchers used microarrays to identify the active genes in breast cancer cells from 159 patients who were followed up after surgery to remove the cancer. They found that patients whose cancer returned or who died during the study period shared 64 active genes in common, but this set of genes was not active in other patients where the cancer did not reoccur. This study showed how microarrays might be used to predict how people with breast cancer will respond to treatments and these ndings may lead to new treatments for cancer. The following box outlines how microarrays work.
Figure 11.29 A scientist holding a microarray on a glass slide. The computer screen
shows an enlargement of just one of the many segments on that microarray. This segment has 20 columns and 20 rows. With 48 such segments in a 4 x 12 arrangement, this microarray would have a total of nearly 20 000 spots. What is present at each spot?
408
HOW DO MICROARRAYS WORK?

Imagine that some research scientists want to identify how gene activity changes when mouse cells are exposed to a particular drug. To do this, the scientists need: 1. a mouse microarray with the single-stranded DNA of the spots coming from genes of the mouse genome 2. two cell samples, one from cells that have been exposed to the drug treatment and the second from normal cells that have not been exposed to the drug treatment. (Why two cell samples?) The next step is to separately extract all the mRNA from each cell population. This mRNA is used as a template to make single-stranded DNA known as copy DNA (cDNA). The unknown cDNA molecules from the two cell samples are labelled with a coloured uorescent marker so that they can later be detected, with a different colour being used for the control cells (green label) and the drug-treated cells (red label). Next, the mixtures of unknown cDNA molecules from both samples are exposed to the microarray.
Gene that strongly increased activity in drug-treated cells Gene that strongly decreased activity in drug-treated cells Gene that was equally active in treated and untreated cells Gene that was inactive in both groups
When a cDNA sequence is complementary to one of the spots on the microarray, the cDNA with its uorescent label binds to this probe. Possible results for one gene are shown in table 11.9.
Table 11.9 Results expected when cDNA from untreated

(control) cells with a green uorescent label and drug-treated cells with a red label are probed using a microarray
Control cells Gene ON Gene ON Gene OFF
Drug-treated cell Gene OFF Gene ON Gene ON
Result on microarray GREEN spot YELLOW spot RED spot
Finally, the microarray is scanned using a confocal laser microscope and the locations of the uorescent spots are identied and displayed on a computer screen (see gure 11.30).
Figure 11.30 Because of the large amount of data

involved, computer software is used to analyse the microarray results. Here we see one segment of a microarray and the information that it provides. Does this result provide evidence that the drug treatment changed the activity of genes in the treated cells compared with the control cells?
Switching genes off

Imagine a situation in which a mutant allele involved in disease occurrence could be switched off. Such a technology might open the way for new approaches to the treatment of disorders that have a genetic component, such as Parkinsons disease, which is apparently caused by the over-production of a particular protein. Such a technology would also open the way to modify economically important animal or plant species, as for example, creating coffee plants that do not produce caffeine by switching off their caffeine-producing genes. In fact, an exciting new technology now exists that can target and selectively switch off active genes.
Silencing genes via RNA interference (RNAi)

The rst clue that it might be possible to switch off or turn down genes came in the 1980s. Scientists tried to intensify the natural purple colour in petunias by adding double-stranded RNA (dsRNA) to petunia cells where one strand of this RNA matched the mRNA transcribed by the pigment-controlling petunia gene. To the scientists surprise, instead of becoming deeper purple, most of the petunias treated in this way turned white. At that time, this result could not be explained.
409
ODD FACT
In 2001, scientists discovered that this method also worked on genes in human cells in test tubes. RNAi has now been demonstrated to exist in many eukaryotes and it may have evolved as a protection against viral infections.
In 1998, an explanation for the petunias emerged from research carried out by biologists at the University of Massachusetts in the United States. They discovered that adding double-stranded RNA (dsRNA) to cells caused some genes to be silenced. In each case, the affected gene was the one that normally transcribed mRNA with a sequence matching one of the strands of the added dsRNA. This nding meant that biologists had developed a means of switching off one or more specic genes in cells. This is called RNA interference (RNAi). RNA interference does not act directly on the DNA of genes but works by breaking down the mRNA produced by one specic gene, leaving all other genes unaffected. RNA interference acts through short fragments of RNA, called small interfering RNA (siRNA). The box below describes how RNAi works.
Potential applications of RNA interference

ODD FACT
Biotechnology companies are exploring the use of siRNAs to treat a form of blindness, known as age-related macular degeneration, that results from excessive growth of blood vessels in the retina. siRNAs will be used to target the mRNA responsible for the protein that stimulates blood vessel growth.
Because siRNAs can be manufactured to target the mRNA made by any gene, RNA interference technology has remarkable potential. In December 2002, the journal Science called RNA interference the breakthrough of the year. Challenges that have yet to be solved include working out how to package siRNAs into a safe and effective form that can be delivered to the relevant cells. Some possible applications of RNAi technology are listed below. In functional genomics, RNAi technology will allow the precise function of genes to be identied by selectively turning them off. Turning off genes can give a clue to their function by seeing the biochemical or physical changes that follow. In medicine, RNAi has the potential to: create new ways of treating human diseases that have a genetic basis, such as Alzheimer disease and various cancers
HOW DOES RNA INTERFERENCE WORK?

The process of switching genes off by RNA interference involves adding long, double-stranded RNA (dsRNA) to a cell. An enzyme, known as Dicer, cuts this RNA into short RNA fragments called small interfering RNA (siRNA). siRNA combines with particular cellular proteins to form an RNAinduced silencing complex (RISC). The RISC is like a homing device that is guided to its mRNA target by the siRNA. The specic target recognised by the RISC is any mRNA molecule that includes a base sequence that is complementary to one strand of the siRNA. The target mRNA is broken down by the RISC complex. When the mRNA produced by a specic gene is destroyed, the protein encoded by the gene concerned cannot be produced and so that gene is effectively silenced or knocked out.
(a)
Long double-stranded RNA Short segments of RNA (siRNA)
Cut by Dicer enzyme
mRNA with RISC complex mRNA degraded by RISC complex
5
RISC
3 AAAAA.....AA
Figure 11.31 (a) Simple mechanism of RNA interference

(b) RNAi in human cells. The nucleus of each cell is shown by its blue uorescent label. siRNAs are revealed by uorescent labels, with the guide strand of each siRNA carrying a red label and the other strand carrying a green label. (Where the two strands overlap, a yellow signal results.) The red guide binds to the target mRNA by complementary base pairing, enabling the RISC to destroy the mRNA.
(b)
410
ODD FACT
When pineapples are affected by frost or are put into cold storage, they release an enzyme that causes the centre of the pineapple to blacken, resulting in economic loss. An Australian company, Benitec, has produced pineapple cells in which the gene that controls enzyme release has been silenced using RNAi and these cells have been cloned to produce pineapples that do not blacken.
generate new classes of drugs to silence specic genes treat inherited single-gene dominant disorders; this could theoretically be done by turning off particular mutant alleles act as a powerful new tool in the treatment of viral diseases, such as HIV/ AIDS, inuenza and SARS, by silencing viral replication genes and/or host receptor genes. In the food industry, RNAi technology could be used to remove allergycausing proteins from foods, such as peanuts, and to remove toxins from wild plants, making them edible. In agriculture, RNAi technology has the potential for use in protecting cereal crops from viral diseases, and could result in new ways of controlling major insect pests of animal and plant crops, such as sheep blowy (Lucilia cuprina), the Queensland fruit y (Batrocera tryoni) and the cotton bollworm (Helicoverpa armigera) by silencing key genes essential for the development or reproduction of these pest species. In conservation, RNAi technology could be used in the control of introduced pest species, such as is occurring with the Daughterless Carp project that aims to silence the gene that produces an enzyme necessary for female sexual development. No hormone, no females (refer back to Nature of Biology Book 1 Third Edition, page 516).
ODD FACT
Anthocyanin pigments (red, pink, mauve and blue) are found in the vacuoles of petal cells. A second major group of ower pigments are carotenoids (yellow, orange) that are found in special plastids, known as chromoplasts.
Case study: Blue roses at last!

In earlier editions of Nature of Biology Book 2, we discussed the attempts by scientists at Calgene Pacic, later to become Florigene Ltd, to produce blue roses through gene manipulation. While the company was successful in producing the worlds rst blue carnations in 1996, the goal of blue roses eluded them. Then, success at last! It was RNA interference that nally enabled scientists from Florigene in Melbourne and scientists at Suntory Ltd in Japan to produce blue roses as announced in mid-2004 (see gure 11.32). For more than 160 years, breeders and scientists have tried to produce blue roses but with no success. How was this nally achieved? The various colours seen in ower petals are due to the presence of coloured pigments. Among these are anthocyanins, such as the red/pink cyanidin pigment and the blue delphinidin pigment. While roses have the gene to produce red pigment, they lack the gene that controls production of an enzyme needed to produce the blue pigment. A simplied version of the pathway for production of these two pigments is shown in gure 11.33. In roses, the genes for enzymes A and C are present, but the gene responsible for the production of enzyme B is absent.
Figure 11.32 A novel coloured

rose containing the blue pigment from delphiniums. These roses were jointly developed by Suntory Ltd and Florigene Ltd as part of their longstanding joint venture. (Image courtesy of Suntory Ltd)
Precursor compound 1 (colourless) Enzyme A Precursor compound 2 (colourless) Enzyme C Cyanidin (pink, red, lilac) Enzyme B Precursor compound 3 (colourless) Enzyme C Delphinidin (blue)
Figure 11.33 Part of the pathway for production of two of the common ower pigments.
Each step is catalysed by an enzyme whose production is controlled by a specic gene. Roses lack the gene responsible for the production of enzyme B.
411
ODD FACT
The rst blue rose contained 97 per cent delphinium pigment and just 3 per cent cyanidin. Scientists are now trying to increase the pH of the rose petals as that will intensify the blue colour. This pH change will make the blue rose appear more blue and less mauve.
The recipe used by the Florigene/Suntory scientists to create a blue rose is shown in gure 11.34: 1. Take a red rose. 2. Silence a rose gene. The gene silenced was the gene responsible for producing enzyme C (see gure 11.33). This gene was silenced using RNA interference (RNAi). A rose with this gene silenced will be white. (Why?) 3. Add a pansy gene. The gene added was the pansy gene responsible for producing enzyme B. Even with this gene, the rose will still be white. (Why?) 4. Add an iris gene. The second gene added was the iris gene responsible for producing enzyme C that converts colourless precursor compound 3 to blue delphinidin pigment. (Because the iris gene is slightly different from the corresponding rose gene, it was not affected by the RNAi.)
RNAi Silence Enzyme C Add Enzyme B 3 Replace Enzyme C
Figure 11.34 The recipe for

creating the blue rose
1
KEY IDEAS
Genes differ in the period over which they are active or being expressed. Some genes act in all living cells, while other genes are active in certain cells only. Microarray technology provides a means of identifying all of the active genes in various cell populations. RNA interference (RNAi) provides a means of selectively targeting and silencing genes. Small interfering RNAs (siRNAs) produced in cells are the active molecules in gene silencing.
QUICK-CHECK
20 List one gene that is expressed at the following times: a only during embryonic development b from adulthood. 21 Are all genes active in all cells? Explain. 22 Identify the following statements as true or false. a Spots on a microarray consist of double-stranded DNA. b Microarrays exist that cover all known genes of the human genome. c Microarrays can be used to compare gene action in cells from different tissues. d RNAi silences a gene by knocking out the mRNA product of that gene. 23 What was the role of the iris gene in the creation of blue roses? 24 What is an siRNA?
412
BIOCHALLENGE
Genes play a role in the structure and function of living organisms. The genetic instructions of all eukaryotic organisms are carried in the DNA of the chromosomes and these are isolated within the nucleus of each cell. The image shown below is the creative work of Drew Berry (refer back to gure 1.34 on page 27). Examine this image and answer the following questions.
2
1
a b c d e f g
6
4
10
What is represented as a yellow strand from panel 2 onwards? Where does the process of transcription occur? In which panel(s) is the process of transcription shown? What is represented as a blue structure from panel 5 onwards? Where does the process of translation occur? In which panel(s) is the process of translation shown? What do the dark red structures from panel 8 onwards represent?
If you are provided with the additional information that mature red blood cells in the circulatory system do not have a nucleus, do you want to modify your answer to question 2?
5
Most of the haemoglobin found in red blood cells is produced in precursor red cells (known as erythroblasts) located in the bone marrow. These precursor cells eject their nuclei before entering the circulatory system as red blood cells. A small amount of haemoglobin continues to be produced in red blood cells for a short time immediately after they enter the circulatory system. How can the production of protein chains continue in these cells in the absence of a nucleus?
2
In which tissue do you think that the processes shown are occurring?
3
Identify each of the following as built of either nucleotides or amino acids: a DNA b RNA polymerase c messenger RNA d ribosome e haemoglobin.
413
CHAPTER REVIEW
Key words
CROSSWORD
alternative splicing amino acids anaemia anti-codon apoptosis base additions base deletions base substitutions beta thalassaemia codons copy DNA (cDNA) deoxyribose DNA arrays DNA-binding proteins DNA ligase DNA polymerase DNA primase
DNA replication gene action gene chips haemoglobins helicase homeotic genes messenger RNA (mRNA) microarrays nucleolar organiser regions (NORs) nucleolus polypeptide post-translation modication protein chains regulator genes
ribonucleic acid (RNA) ribose ribosomal RNA (rRNA) ribosomes RNA interference (RNAi) RNA polymerase semi-conservative model small interfering RNA (siRNA) structural genes thymine transcription transfer RNA (tRNA) translation uracil
Questions
1 Making connections Use at least eight of the key words from this chapter to form a map for the concept gene action. In drawing your map, add any other concepts that you wish. 2 Demonstrating understanding The following is part of the nucleotide sequence in the template strand of part of a gene: . . .T A T G G G C A T G T A A T G G G C . . . a Identify the base sequence in each of the following: i the complementary DNA strand ii the mRNA that would be transcribed from this template. b How many codons are present in this mRNA? c List the anti-codons that correspond with each codon. 3 Applying knowledge Refer to the genetic code (see table 11.4) and answer the following questions: a Which codons in mRNA control the addition of the amino acid, gly? b How many codons contain the information to add the amino acid, lys, to a protein? For each codon, write the complementary anti-codon. c When the mRNA codon, UUU, is translated, which amino acid is added to a protein chain? 4 Demonstrating understanding A protein includes the following amino acids in part of its structure: . . . - val - thr - lys - pro - . . . a How many codons are needed for the instruction to put these amino acids into place? b Write this instruction in genetic code, as it would appear in mRNA. Would you predict that your code would be identical to that written by all your fellow students? Explain.
414
5 Developing logical explanations Suggest explanations for the following: a Beta thalassaemia affects the production of haemoglobin A but does not affect haemoglobin A2 or F. b The change of just one base in a genetic instruction that consists of more than 1000 bases can be lethal. c Forensic scientists can distinguish between human fetal blood and adult blood. d A mutation in one gene disrupted embryonic development in an insect and caused legs to appear in place of antennae. 6 Analysing information and drawing conclusions A mutation in one gene (G1) affects just one kind of protein produced by a cell. A mutation in another gene (G2) affects a large number of different kinds of proteins produced by that cell. One of these genes carries the coded instructions to make one kind of tRNA. The other carries coded information to make one kind of salivary enzyme. Which is more likely to be the gene for the tRNA, G1 or G2? Explain. 7 Analysing information and drawing conclusions A form of thalassaemia exists in which no alpha chains are produced. This condition is known as alpha thalassaemia. Refer to table 11.1 (page 386) and suggest possible answers to the following: a The effects of beta thalassaemia do not appear until after birth. Would the same be expected to be true of alpha thalassaemia? Explain. b Which haemoglobin(s) would be affected in a case of alpha thalassaemia? 8 Demonstrating understanding A segment of mRNA has the base sequence ...CAU AAG AAU CUU GC... a Write the DNA base sequence that produced this mRNA. b Write the four amino acids that would be translated from the beginning of this mRNA segment. c Assume that a base substitution occurs in the original DNA so that the third base (U) of the mRNA is replaced by a G: . . . C A G* A A G A A U C U U G C . . . Write the amino acid sequence that would result from this change. d Assume that a base addition occurs in the original DNA so that a G is added between the third and fourth bases: . . . C A U G*A A G A A U C U U G C . . . Write the amino acid sequence that would result from this change. e On the basis of this information, what kind of change in DNA has a more extensive effect on the protein resulting from gene translation a base substitution or a base addition? Explain. 9 Applying knowledge a Where is it? Where would you find the following: i a codon? ii gene transcription in action? iii an anti-codon? iv gene translation in action? v rRNA? b What is it? Suggest possible identities for the following: i a STOP codon ii a START codon
415
an amino acid that has six codons a self-replicating molecule that carries information in coded form the cell organelle to which a mRNA molecule attaches for translation. 10 Developing logical explanations Examine figure 11.35 which shows kernels on a corn cob. A corn cob is a collection of offspring from a pair of parents. Notice that some of the kernels are full and swollen, while a smaller number are wrinkled and shrunken. This variation is due to the action of a single gene with two alleles.
iii iv v
Figure 11.35
Suggest how the action of the alleles of this gene might give rise to these two phenotypes. (Your answer should make reference to an enzyme.) 11 Applying knowledge and understanding Haemophilia can be caused by many different kinds of changes to the F8C gene. The F8C gene on the X chromosome consists of 26 exons and 25 introns. a In some families, haemophilia results from deletion of a portion of the F8C gene. Suggest how a deletion could produce haemophilia. b In other families, the haemophilia results from a change in one base in the F8C gene. Suggest how a base substitution could produce haemophilia. c In other families, the haemophilia is due to the insertion of a long piece of repetitive DNA into the F8C gene. Suggest how an insertion could produce haemophilia. d When the F8C gene is transcribed, is all the DNA of the gene transcribed? e When the F8C gene is translated, is all the DNA of the gene translated? 12 Using the web Go to www.jaconline.com.au/natureofbiology/natbiol2-3e and click on the DNA replication weblink for this chapter. a Read the introduction, then click on Replication advanced. b From the next frame, you can check on some of the details of DNA replication. By clicking on the symbols at the right-hand side, you can watch animations of replication of the leading strand and replication of the lagging strand. i In what direction does the lagging strand run? ii Which strand replicates in a continuous manner? in a discontinuous manner? c Classify the following components as a place or as an enzyme or as neither: i replication origin ii replication fork iii DNA helicase iv RNA primer v DNA polymerase.
416
13 Using the web Go to www.jaconline.com.au/natureofbiology/natbiol2-3e and click on the Cystic fibrosis weblink for this chapter. a Identify the following information about the gene that causes the genetic disorder cystic fibrosis: i Official name of gene ii Gene symbol iii Locus iv Size of gene (bp) v Size of pre-mRNA transcript (bp) vi Size of mRNA (bp) vii Size of the coding sequence of mRNA (bp) viii Size of protein product (amino acids) ix Protein function. b Answer the following questions about the gene that causes cystic fibrosis. i How many exons are there in the DNA of this gene? ii The pre-mRNA is longer than the mRNA. Explain. iii The coding sequence within the mRNA is shorter than the mRNA. Explain. iv What relationship exists between the number of bases in the coding sequence of the mRNA and the number of amino acids in the protein product? 14 Interpreting information In Mendelian genetics, we focus on variation in phenotypes. So, when we think about a gene that is responsible for an inherited disorder, we typically assign just two alleles for example, the TYR gene has allele A for normal pigmentation and allele a for albinism. However, at the level of its DNA, one gene can have a very large number of different alleles. Every nucleotide change in the DNA of a gene is a different allele of that gene. These changes include base substitutions, base additions or deletions, and inversions. a What is a base substitution? b How does a base substitution differ in its effect on the protein product of the gene from a base addition? 15 Using the web Go to www.jaconline.com.au/natureofbiology/natbiol2-3e and click on the CFTR weblink for this chapter. From the menu in the lefthand column, click on View List (under Allelic Variants). This list shows just some of the different alleles of the CFTR gene for example: single base substitution CFTR, ALA455GLU indicates that the 455th base in the CFTR gene has been changed so that, instead of coding for ALA, a GLU instead goes in the protein chain. base deletion CFTR, 1BP DEL. 557T indicates that the 557th base in the normal gene, which is a T, has been deleted. base addition CFTR, 1-BP INS, 2869G indicates that an insertion (addition) of one G nucleotide has occurred at the 2869th nucleotide of the gene. Other mutations include inversions, shown as INV. a Scan the list of CFTR alleles. What is the most common type of mutational change? b Explain the meanings of CFTR, PHE507DEL and CFTR, ARG117HIS.
417

Chapter 11

Transféré par

Informations du document

Description originale:

Titre original

Copyright

Formats disponibles

Partager ce document

Partager ou intégrer le document

Options de partage

Avez-vous trouvé ce document utile ?

Ce contenu est-il inapproprié ?

Droits d'auteur :

Formats disponibles

Chapter 11

Transféré par

Droits d'auteur :

Formats disponibles

11

Gene function: genes in action

Sea in the blood

Meet a family and its genes

Figure 11.2 Photomicrograph

Figure 11.3 In this family only

Haemoglobin and its chains

Table 11.1 Chains present in

Type of haemoglobin haemoglobin A

Usual occurrence major post-birth haemoglobin

Chains present 2 alpha chains 2 beta chains

minor post-birth haemoglobin

2 alpha chains 2 delta chains

major fetal haemoglobin

2 alpha chains 2 gamma chains

Symptoms of beta thalassaemia

Figure 11.4 A slow-infusion pump

Treating beta thalassaemia

The HBB gene

Figure 11.5 The HBB gene

NATURE OF BIOLOGY BOOK 2

Figure 11.6 Soltirios

GENE FUNCTION: GENES IN ACTION

Figure 11.7 The nucleus is where

NATURE OF BIOLOGY BOOK 2

Transcription: copying the original

DNA and RNA compared

Table 11.2 Summary of differences

Feature sugar in nucleotide sub-unit bases in nucleotide sub-unit usual structure

DNA deoxyribose A, G, C and T double-stranded chain forming a double helix ribose

A, G, C and U single-stranded chain

Figure 11.8 (a) Representation of

Figure 11.9 Because of pairing

From DNA to mRNA: step by step

Figure 11.10 Transcription occurs

Free ribonucleotides A G U G C U G U A U A C G U C A A T A AA TT T A C G RNA polymerase

Pre-mRNA is modi ed after transcription

Translation: decoding genetic instructions

Anticodoncodon base pairing

From mRNA to protein: step by step

Figure 11.13 (a) Transfer RNA

NATURE OF BIOLOGY BOOK 2

mRNA codon UUU UUC UUA UUG CUU

Amino acid phe

mRNA codon UCU UCC

mRNA codon UAU

Amino acid tyr

mRNA codon UGU

Amino acid cys

CUC CUA CUG AUU

AUC AUA AUG GUU GUC GUA GUG

Figure 11.14 (a) The mRNA

(b) mRNA GGGCUGCAA C C C GA C

GENE FUNCTION: GENES IN ACTION

Putting it all together: transcription and translation

Transcription Polypeptide chain Polymerase Amino acid mRNA Nucleus

Figure 11.15 Representation

Alternative splicing of pre-mRNA

NATURE OF BIOLOGY BOOK 2

Figure 11.16 Alternative splicing

(b) EXON JUGGLING Intron Exon Exon Intron Exon

Comparing prokaryotes and eukaryotes