Chromosome and DNA

13.1Morphology of chromosomesOften examined

Mendel's hereditary factors were an abstract idea. At that time no cellular structure was known that could house them. We now know that these factors are genes, that genes lie on chromosomes, and that genes are made of DNA. This chapter studies chromosomes and DNA in detail.

Chromosomes are thick, thread-like structures that appear in the nucleus during cell division. In an interphase cell the chromosomes are uncondensed and look like a very fine network called the chromatin network.

Structure of chromosome

A typical chromosome consists of two strands called chromatids. Each chromatid is made of one long DNA molecule that is highly coiled together with histone proteins, and the chromatids contain the genes for different traits. Both chromatids are attached to each other at a point called the centromere, so each chromosome shows two arms.

Chromatid

One of the two strands of a chromosome; it is made of a single, highly coiled DNA molecule with histone proteins and carries genes.

Centromere (primary constriction)

The point at which the two chromatids are attached to each other. It divides the chromosome into two arms.

Arm

The region of the chromosome from the centromere to an end.

Secondary constriction (nucleolar organizer)

Another point of union along the length of the chromatids in some chromosomes. It gives rise to nucleoli during interphase. At least one pair of homologous chromosomes has a nucleolar organizer region.

Satellite

The knob-like end that lies beside the secondary constriction. This region has a useless sequence of DNA called junk DNA.

Telomeres

The terminal ends of a chromosome. They prevent two chromosomes from attaching to each other by their ends.

Types of chromosomes

On the basis of the position of the centromere along the chromosome, a chromosome may be metacentric, submetacentric, acrocentric or telocentric.

13.1Composition and organization of chromosomeOften examined

Generally a chromosome is made of 40% DNA and 60% protein. In a cell that is ready to divide, the chromosome has two identical DNA molecules, so each chromatid has one DNA molecule. An average-sized human chromosome has DNA about 5 cm long, which consists of about 140 million nucleotides. How such a huge molecule fits into a tiny chromosome is explained by the way it is packed.

DNA is a negatively charged molecule because of its phosphate groups. It therefore has a strong affinity for histone proteins, which are positively charged (unlike many other proteins) because they contain many basic amino acids such as arginine and lysine.

During the S phase of the cell cycle, DNA and histones are completely disorganized from each other. After DNA is replicated, DNA and histones organize together again, and the condensation continues until the cell divides and the chromosomes appear. The organization of chromosomes occurs in four levels.

Level 1: nucleosome string

Just after DNA replication, each DNA molecule begins to coil around histone cores. Approximately every 200 nucleotides of the duplex DNA wrap twice around a core of eight histones. This complex is called a nucleosome. One histone molecule (histone H1) is associated with a small segment of DNA, the linker DNA, between every two nucleosomes. In this way the whole DNA (2 nm thick) becomes a chain of beads called the nucleosome string (10 nm thick), the "beads on a string" form of chromatin.

Level 2: chromatin fibre

Immediately afterwards, the nucleosome string coils again about its axis to form a thicker fibre of 30 nm, called the chromatin fibre. During the G₁ and G₂ phases, chromosomes are found at this level of organization. The chromatin fibre shows two regions: heterochromatin and euchromatin.

Level 3: supercoil

When cell division begins, the higher-order coiling of the chromatin fibre gives rise to the supercoil, which has a diameter of 300 nm.

Level 4: chromatids

The supercoil immediately establishes itself into the chromatid of 700 nm as a result of further coiling around itself. The two chromatids together form the chromosome (about 1400 nm wide).

13.2DNA as the hereditary materialOften examined

When the chromosomal theory of inheritance was confirmed in 1910, geneticists began to ask in what form the heredity units are found in the chromosome. Chromosomes contain both DNA and protein, so on which of these is the hereditary information written? Over a period of about 30 years, starting in the late 1920s, a series of investigators addressed this question.

Griffith's experiment

In 1928 the British microbiologist Frederick Griffith made a series of unexpected observations while experimenting with Streptococcus pneumoniae. This bacterium is found in two types.

S-type

Forms a polysaccharide capsule, so its colony looks smooth and shiny. It is virulent (disease-causing).

R-type

Has no polysaccharide capsule, so its colony is rough. It is non-virulent (benign).

Griffith concluded that somehow the information specifying the polysaccharide capsule and virulence had passed from the heat-killed S-type bacteria to the living R-type bacteria in the mixture, transforming them into living S-type virulent bacteria that killed the mice. This transfer of genetic material from one organism to another, by which the genetic make-up of the recipient is altered, is called transformation.

Extra reading material: experiment of Avery, Macleod and McCarty

The agent responsible for transforming R-type to S-type was undiscovered until 1944. In a classic series of experiments, Oswald Avery with Colin Macleod and Maclyn McCarty characterized what they called the "transforming principle". They first took the extract (filtrate) of heat-killed S-type bacteria, which contained carbohydrates, lipids, protein, RNA and DNA. They divided this extract into four samples.

Therefore it was confirmed that the active factor, which caused transformation of live R-type into live S-type in Griffith's experiment, must be DNA.

13.2Hershey and Chase experimentOften examined

Soon after Avery's results, another very convincing experiment on bacteriophages was performed by Alfred Hershey and Martha Chase in 1952.

Bacteriophages are viruses that attack bacteria. Their body consists of DNA and protein. During infection they multiply in the host and many copies of them emerge within 20 to 25 minutes. Until 1952 it was not known whether DNA or protein carries the hereditary information of bacteriophages. Scientists were not even sure whether, during infection, the whole viral particle enters the host or only its DNA or protein gets in. Hershey and Chase set out an experiment for this purpose.

13.3Models of DNA replicationOften examined

The process of self-synthesis of a DNA molecule is called DNA replication. This process occurs only once, in the S phase of the life cycle of a cell. The DNA molecule that is replicated is called the parent DNA, and the molecules produced in this process are called daughter DNA. One parent DNA molecule gives rise to two daughter DNA molecules.

Models of DNA replication

How can duplex DNA replicate? Scientists tried to answer this after the discovery of the structure of DNA. Three different models were presented to explain the replication process: the semi-conservative, conservative and dispersive models.

Semi-conservative model

The two parental DNA strands separate, and each strand serves as a template for the synthesis of a new DNA strand. The result is two DNA double helices, each of which consists of one parental and one new strand.

Conservative model

After replication one daughter molecule contains both parental DNA strands, and the other daughter molecule contains DNA strands of all newly synthesized material.

Dispersive model

During replication the parental DNA molecule is dispersed (broken) into its nucleotides; these nucleotides combine with new nucleotides to form two new daughter DNA molecules, each a mixture of old and new DNA.

13.3Meselson and Stahl experimentOften examined

The three models were evaluated by Matthew Meselson and Franklin Stahl of the California Institute of Technology in 1958. They were later awarded a Nobel Prize. From their experiment it was finally concluded that the replication of DNA occurs according to the semi-conservative model.

On the basis of these results Meselson and Stahl claimed that DNA replication is semi-conservative.

13.3Mechanism of DNA replicationOften examined

Although DNA replication is a continuous process, it is discussed in different phases for convenience: the initiation phase, the extension (polymerization) phase and the termination phase.

Initiation phase

The initiation phase is characterized by the formation of the replication bubble and the replication fork at a particular site called the origin of replication. This is a specific sequence of nucleotides along the length of the DNA from where replication begins. Eukaryotic DNA may have more than one origin of replication, but prokaryotic DNA has only one.

The replication bubble is formed when the enzymes DNA helicase and DNA gyrase work at the origin of replication.

• DNA helicase opens the turns of the DNA duplex by breaking down the base pairs so that the two DNA strands can be separated.
• DNA gyrase works slightly ahead of the helicase and facilitates the unwinding of the DNA duplex by reducing the tension created during unwinding.
• Because of these two enzymes the two strands gradually separate and give a bubble-like appearance at the origin of replication: the replication bubble.
• After the base pairs are broken, the single strands are prevented from pairing up again by specific proteins called single-stranded binding (SSB) proteins.
• Both single strands act as template strands in the next phase and direct the synthesis of the daughter strands along themselves. Each side of the replication bubble is now called a replication fork.

Extension (polymerization) phase

Extension is the formation of the daughter strands (leading or lagging strands) along the template strands. The daughter strands are actually synthesized by the enzyme DNA polymerase. This enzyme cannot work unless some nucleotides are already arranged on the template. For this purpose the enzyme primase arranges some RNA nucleotides on the template strands. Such short fragments of a few RNA nucleotides are called primers; they act as the start site for the activity of DNA polymerase. The primase and DNA helicase enzymes are found together in a complex called the primosome.

After the primers are established, synthesis of the daughter strands begins by DNA polymerase. There are three different forms of this enzyme.

Mechanism of DNA polymerase III activity

DNA polymerase III cannot initiate the replication process. It can add a nucleotide only onto a pre-existing 3′-OH group. Therefore it needs a primer to perform its polymerase activity. It always adds nucleotides at the 3′ end of the primer, so the direction of replication is always 5′ to 3′.

One unit of DNA polymerase III works on one template and continuously synthesizes a daughter strand towards the replication fork. This continuously growing daughter strand is called the leading strand. The second unit works on the other template. It synthesizes the other daughter strand away from the replication fork. As the two units are interlinked, the second unit is allowed to polymerize the daughter strand only up to a specific length (100 to 200 nucleotides in eukaryotes and 1000 to 2000 nucleotides in prokaryotes), and then it has to jump back to a new primer to perform polymerization again. Therefore this daughter strand grows discontinuously, away from the fork, as short fragments interrupted by primers. These fragments are called Okazaki fragments (named after the Japanese scientist who discovered them), and this discontinuously growing strand is the lagging strand.

One subunit of DNA polymerase III also has the ability to remove a wrong nucleotide if it is added by mistake. This ability is called proofreading.

Termination phase

The termination phase is characterized by the replacement of the RNA primers with DNA nucleotides by DNA polymerase I. The resulting segments are joined by DNA ligase, which forms phosphodiester bonds.

13.3DNA stability and variability

Replication has to do two opposite jobs. It must copy the base sequence faithfully (stability), and yet occasional errors in copying are the source of new genetic variations (variability). The book describes both as characters of the replicating DNA molecule.

DNA stability

The conservation of DNA sequences through numerous cell divisions, ensured by DNA polymerase II and III.

DNA variability

The production of genetic variations by mutations in the base sequence that result from errors during DNA replication.

13.4Gene expressionOften examined

DNA is the genetic material, which can replicate. The genetic material is in the form of specific sequences of nucleotides along the DNA strands. The DNA inherited by an organism forms specific traits by directing the synthesis of a protein that acts as a catalyst and catalyses a specific chemical reaction of the cell. Thus a gene expresses itself in a protein or enzyme that controls the development of a specific character or function. We can say that proteins are the link between the genotype and the phenotype.

Gene expression or protein synthesis includes two processes: transcription and translation.

Central dogma of molecular genetics

The idea that DNA makes protein via an intermediate RNA. It involves two processes: transcription (DNA to RNA) and translation (RNA to protein).

Transcription

The synthesis of RNA from DNA. It is the first step of gene expression.

Translation

The synthesis of a polypeptide (protein) by the ribosome, using the information in the mRNA made by transcription. It is the second step of gene expression.

13.4TranscriptionOften examined

Transcription is the synthesis of RNA from DNA. It is the first step of gene expression. It occurs in the G₀, G₁ and G₂ phases of the cell cycle. It requires only one enzyme, RNA polymerase. It is a continuous process, but for convenience it is divided into three phases: initiation, elongation and termination.

Initiation phase

Transcription begins with the binding of RNA polymerase at the promoter region, a regulatory region of the gene that comprises binding sites for the attachment of RNA polymerase. The names of the sequences (−10, −35, −25, −80, −90) refer to their position in the promoter: about how many nucleotides before the transcription start point of the gene they lie.

RNA polymerase of prokaryotes consists of four subunits: two alpha (α) and two beta (β) subunits, called the core enzyme, while the sigma factor is required for RNA polymerase to bind on the promoter. The core enzyme and sigma factor together constitute a holoenzyme. Once RNA polymerase is attached to the promoter, the sigma factor is removed and the core enzyme catalyses the remaining process.

• Like DNA polymerase, RNA polymerase adds nucleotides to the 3′ end of the growing chain, but unlike DNA polymerase it does not require a primer to start polymerization.
• In prokaryotes only one type of RNA polymerase is found.
• In eukaryotes there are three types: RNA polymerase I synthesizes rRNA, RNA polymerase II synthesizes mRNA, and RNA polymerase III synthesizes tRNA.

As RNA polymerase binds to the promoter, the DNA duplex unwinds, base pairs are broken and a bubble-like structure, the transcription bubble, appears.

Elongation phase

As RNA polymerase binds to the promoter, it begins to arrange and polymerize ribonucleoside triphosphates (rNTP, ribonucleotides) complementary to the template strand of the DNA. It does not need a primer to start. One of the two strands of the gene acts as the template.

Template strand (antisense strand)

The strand of the gene copied by RNA polymerase. It is called antisense because the mRNA is complementary to it.

Coding strand (sense strand)

The other strand of the gene. Its sequence is the same as the mRNA (with U in place of T).

In the elongation phase RNA polymerase keeps moving from the 5′ to the 3′ end of the RNA, towards the terminator region of the gene. The transcription bubble also moves along the DNA, leaving the growing RNA strand protruding from the bubble. This continues until the RNA polymerase reaches the terminator region of the gene.

Termination phase

The sequence of the terminator region of the gene stops the synthesis of mRNA. The terminator region consists of a series of GC base pairs followed by a series of AT base pairs. The part of the mRNA transcribed in this region projects to form a loop-like structure called the GC hairpin, followed by a small tail of poly-U nucleotides. The GC hairpin causes the RNA polymerase to stop the synthesis of RNA.

13.4Post-transcriptional modification of mRNAOften examined

In prokaryotes there is no delay between transcription and translation: the mRNA emerges from the DNA and is translated at once, because there is no definite nucleus. In eukaryotic cells the pre-mRNA (newly synthesized mRNA) has to be modified into mature or functional mRNA, because transcription occurs in the nucleus while translation occurs in the cytoplasm. The mRNA has to move from the nucleus to the cytoplasm, and during this journey enzymes such as phosphatases and nucleases may degrade it. Eukaryotic mRNA also contains some non-coding regions called introns, which are removed (spliced) during this process.

Post-transcriptional modification therefore involves two events: addition of a cap and tail to protect the mRNA from degradation, and RNA splicing to remove non-coding sequences.

Cap

7-methyl GTP linked from its 5′ to the 5′ end of the mRNA.

Poly-A tail

A small chain of 30 to 500 adenine nucleotides attached to the 3′ end of the mRNA. The cap and tail prevent the mRNA from being degraded by phosphatases and nucleases.

RNA splicing

The removal of introns and maturation of the primary mRNA to secondary (functional) mRNA. It is catalysed by spliceosomes, a large RNA-protein complex. The exon fragments are then joined with the help of RNA ligase enzyme.

Exon

A coding segment that stays in the mature mRNA.

Intron

A non-coding segment that is removed during splicing.

13.4Genetic codeOften examined

A gene is a specific segment of DNA that encodes the synthesis of a particular polypeptide (protein). Therefore the order of amino acids in a polypeptide is according to the sequence of nucleotides in a part of DNA. This relationship between the amino acid sequence and the nucleotide sequence is called the genetic code. In other words, the information in DNA for the synthesis of protein, which is transcribed (copied) into mRNA, is called the genetic code.

The mRNA transcript consists of a random sequence of only four kinds of nitrogenous bases (A, G, C and U). How can a code with a four-letter alphabet specify a protein that contains one of twenty different amino acids at any point? A single base cannot specify a single amino acid: only four amino acids could be encoded, and proteins with only four different amino acids would be formed. Two bases are also not feasible, since only 16 amino acids could be encoded ($4\times 4=16$). Three bases are sufficient: a total of $4\times 4\times 4=64$ combinations are possible, and each is specific for a particular amino acid. Therefore a triplet of bases along the length of mRNA that specifies a particular amino acid is called a codon.

• There are 64 codons in total.
• Three of them, UGA, UAG and UAA, are stop codons. One of these must be present at the end of the mRNA to show that the message is over. They do not encode any amino acid, so they are called nonsense codons.
• All the other codons encode specific amino acids and are called sense codons.
• One sense codon, AUG (methionine), also acts as the start codon, which must be present at the beginning of every sequence that codes for an amino acid chain.

Characteristics of the genetic code

1. Degenerate. Some amino acids are encoded by only a single codon, while others are encoded by up to four codons, and the amino acids leucine and serine are encoded by six codons. This property is known as code degeneracy.
2. Universal. The code is the same in almost all organisms. For example, AGA specifies arginine in bacteria, in humans and in all other organisms whose genetic code has been studied. Because of this universality, genes can be transferred from one organism to another and be successfully transcribed and translated in their new host. The study of the genetic code of mitochondrial DNA, however, showed that the code is not universal: UGA, normally a stop codon, reads as tryptophan in mitochondria; AUA is read as methionine instead of isoleucine; and AGA and AGG are for termination of protein synthesis instead of arginine.
3. No punctuation. There is no punctuation between codons: there is no gap between two codons.
4. Non-overlapping. The mRNA sequence AUGAGCGCA is not read as AUG / UGA / GAG and so on; it is read as AUG / AGC / GCA.
5. Triplet. Each codon is made of three bases.

13.4TranslationOften examined

Translation is the second step of gene expression. In translation, the messenger RNA (mRNA) produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein.

Translation is a continuous process, but for convenience it is discussed in four phases: activation of amino acids, formation of the initiation complex, elongation and termination.

Activation of amino acids

Activation of amino acids is the binding of free amino acids dispersed in the cytoplasm to the 3′ end of particular tRNA molecules. In this way a complex called the aminoacyl-tRNA complex is formed. The binding is catalysed by the enzyme aminoacyl-tRNA synthetase (the activation enzyme). The various amino acids that are to take part in polypeptide formation are continuously activated throughout translation.

Formation of the initiation complex

The process of translation actually begins with the formation of the initiation complex, which is formed by the combination of the ribosomal subunits, the mRNA and the first aminoacyl-tRNA complex.

P site (peptidyl site)

The region of the ribosome where the first aminoacyl-tRNA complex is attached; peptide bonds are formed here between successive amino acids during elongation.

A site (aminocyl site)

The site where successive tRNAs bearing amino acids are attached.

E site (exit site)

The site where empty tRNAs leave the ribosome during elongation.

Polypeptide elongation

In this phase the ribosomal units move along the mRNA, amino acids are brought by tRNAs, and they are joined together to form a polypeptide chain. This is accomplished by three steps, which are repeated again and again throughout this phase.

Termination

Elongation continues until a chain-terminating stop codon (UAG, UAA or UGA) is exposed at the A site. Stop codons do not bind to any tRNA, but they are recognized by release factors that terminate translation. The polypeptide is released from the tRNA, the tRNA is released from the ribosome, and the ribosomal subunits separate from the mRNA.

Difference between translation in prokaryotes and eukaryotes

13.4Fate of synthesized protein

After termination of translation, the polypeptide chain folds and forms a three-dimensional protein shape. It then enters the Golgi complex for further modifications. The protein can be used within or outside the cell that synthesized it.

13.5Regulating gene expression

The overall process by which genetic information flows from genes to proteins, that is, from genotype to phenotype, is called gene expression. Regulation of gene expression is the control of the amount and timing of the appearance of a gene's product. All the cells of a living body must continually turn genes ON and OFF in response to signals from their external and internal environment.

The mature human body is composed of about 200 different cell types. The differences between cell types are due not to different genes being present, but to differential gene expression: the expression of different genes by cells with the same genome.

Importance of regulation of gene expression

• It is essential for both prokaryotes and eukaryotes, as it increases the versatility and adaptability of an organism by allowing the cell to express a protein only when it is needed.
• All the cells of a living body must regulate which genes are expressed at any given time, turning genes ON and OFF in response to signals from the external and internal environment.
• It gives the cell control over all structure and function, and is the basis for cellular differentiation and morphogenesis of any organism.
• When the regulation of gene expression is disturbed, serious imbalances and diseases, including cancer, can arise.

13.5Methods of regulation of gene expressionOften examined

There are two possible ways of regulating gene expression: positive regulation and negative regulation. Some genes are controlled by positive regulation and others by negative regulation.

Positive gene regulation

The expression of genes is quantitatively increased by the presence of a specific regulatory protein, the activator. When the activator is attached with RNA polymerase, it starts the process of transcription.

Negative gene regulation

The expression of genes is diminished by the presence of a specific regulatory protein, the repressor. The repressor protein attaches to the operator, the DNA site next to the promoter, and so stops RNA polymerase from transcribing the gene.

13.5Lac operon

A classic example of gene regulation in bacteria is the lac operon, which demonstrates both positive and negative regulation. The lac operon is a group of genes responsible for the breakdown of lactose, a sugar, into energy. In bacteria, genes are often organized into operons, which are clusters that encode proteins necessary for coordinated functions. The RNA transcribed from these operons is polycistronic, meaning it can encode multiple proteins within a single transcript.

The lac operon consists of a regulatory gene (the i gene) and three structural genes (z, y and a).

This operon shows how cells manage resources efficiently by producing proteins only when necessary, such as in the presence of lactose.

13.6MutationsOften examined

A gene mutation is a permanent change in the DNA sequence that makes up a new allele in the population. Mutations range in size from a change in a single DNA nucleotide, to a large segment of a chromosome or a whole chromosome, or sometimes changes in the number of chromosomes.

Mutation

A permanent change in the DNA sequence (it may range from one nucleotide to a whole chromosome or a change in chromosome number).

Mutagen

An agent that causes mutations.

Mutant

The organism or cell in which a mutation occurs.

Mutagenesis

The creation or origin of a mutation.

Sources of mutagens

The sources of mutation may be physical, chemical and biological agents.

Types of mutation

Creation or origin of a mutation is called mutagenesis. Based upon mutagenesis there are two types of mutations. On the basis of where the mutations occur and to what extent, there are two further types.

13.6Importance of mutation

A mutation may be harmful or useful.

Harmful aspects of mutation

A mutation that decreases the fitness of the organism in its environment is called a harmful mutation. Examples given in the book:

• A person born without a part of the brain.
• Cancer, which is a form of harmful mutation.
• Developmental abnormalities such as microcephaly, cleft palate, and cases of abnormal number of chromosomes (Down syndrome, Klinefelter syndrome, Turner syndrome and so on).
• Hereditary disorders such as sickle cell anaemia and phenylketonuria.

Useful aspects of mutation

Mutations are also considered as contributing factors towards evolution. Changes in the genes controlling development can have major effects on the morphology of the adult organism. Because these effects are so significant, scientists suspect that changes in developmental genes have helped bring about large-scale evolutionary transformations. Developmental changes may help to explain, for example, how some hoofed mammals evolved into ocean-dwellers, how water plants invaded the land, and how small armoured invertebrates evolved wings.

Mutations are considered the driving force of evolution, where less favourable (or deleterious) mutations are removed from the gene pool by natural selection, while more favourable (beneficial or advantageous) ones tend to accumulate.

Critical thinking: how harmful mutations are eradicated by nature

A harmful mutation is a mutation that decreases the fitness of the organism. The eradication of harmful mutations is done by natural selection. The process of DNA repair is an important way in which the body protects itself from disease. Every harmful mutation is eliminated from the population by premature death or reduced reproductive success, a "genetic death".

13.6Chromosomal mutationOften examined

Changes in the structure or number of chromosomes are called chromosomal mutations or chromosomal aberrations. Here the symptoms, causes and possible treatments of three of them are discussed: Down syndrome, Klinefelter syndrome and Turner syndrome.

Down syndrome

• Chromosomes: 2n+1; an extra copy of chromosome 21 (trisomy 21), so 47 chromosomes.
• Symptoms: abnormally shaped, smaller head; rounded inner corner of the eyes instead of pointed; excess skin at the back of the neck; flattened nose; single crease in the palm of the hand; small ears; small mouth; wide, short hands with short fingers; white spots on the coloured part of the eye; excessive space between the large toe and the second toe. The affected people may be male or female.
• Cause: autosomal non-disjunction, in which the 21st chromosomal pair fails to segregate properly during maternal meiosis and results in the formation of an egg having 24 chromosomes. Fertilization of such an egg by a normal sperm containing 23 chromosomes produces a child with 47 chromosomes (2n+1) with three copies of chromosome 21, so it is also called trisomy 21.
• Treatment: there is no treatment for Down syndrome, as it is a chromosomal abnormality. It can be managed to some extent by regular check-ups and screening, medications, surgery, and counselling and support.

Klinefelter syndrome

• Chromosomes: 2n+1 (44+XXY); an extra X chromosome. The patients show trisomy in sex chromosomes.
• Symptoms: several feminine characters although they are males: sparse body hair, enlarged breasts, wide hips, and testicles remain small. The voice may not be as deep. Abnormal body proportions (long legs, short trunk, shoulders equal to hip size).
• Cause: non-disjunction of the sex chromosome pair during maternal meiosis.
• Treatment: testosterone can be given for sexual development, like males, around the age of puberty; it can help a boy have more normal body development. The treatment usually continues throughout a man's life but does not help infertility.

Turner syndrome

• Chromosomes: 2n-1 (44+XO = 45); one of the X chromosomes is absent. The affected individuals are females.
• Symptoms: shorter than average height, infertility, a webbed neck, a low hairline at the back of the neck, abnormal bone development (especially of the bones of the hands and elbows), a larger than usual number of moles on the skin, and oedema (extra fluid) in the hands and feet.
• Cause: non-disjunction of the sex chromosome pair during maternal meiosis.
• Treatment: there is no specific treatment, as it is a chromosomal abnormality. Growth hormone treatment can improve growth and influence a girl's final adult height, especially if started early in childhood. Estrogen replacement treatment helps girls develop the physical changes of puberty, including breast development and menstrual periods; it is often started when a girl reaches about age 12 or 13.

13.6Gene or point mutationsOften examined

A gene or point mutation arises as a result of a base change in an individual gene. It may include base substitution (replacement of one base by another), insertion (addition of one or more bases) and deletion (removal of one or more bases). Frame shift mutations occur when one or more nucleotides are either inserted or deleted from DNA. This results in a completely new sequence of codons and a non-functional protein.

Sickle cell anaemia

Sickle cell anaemia is also known as haemoglobin SS disease (Hb SS) or sickle cell disease.

• Symptoms: painful episodes which can last from hours to days. When the anaemia becomes more severe, symptoms may include fatigue, paleness, fever and rapid heart rate, shortness of breath, jaundice and damage to various organs.
• Cause: a defect in haemoglobin. The sixth amino acid, glutamic acid, in the beta chain of normal haemoglobin is replaced by valine. In the beta chain gene the glutamic acid code (CTT) is substituted by CAT, which codes for valine. The abnormal sickle cell haemoglobin is called Hb^{\mathrm{S}}; it has lost the oxygen-binding capacity, so the red blood cells become sickle shaped and deliver less oxygen to the body's tissues. Sickle cell anaemia is due to a recessive gene: one gets the disease if it is inherited from both parents.
• Treatment: blood transfusions, medicines to relieve pain and plenty of fluids. Bone marrow or stem cell transplants can cure sickle cell anaemia. Folic acid supplements should be taken.

Phenylketonuria (PKU)

A rare condition in which a baby is born without the ability to properly break down an amino acid called phenylalanine is called phenylketonuria.

• Symptoms: lighter skin, hair and eyes; delayed mental and social skills; head size significantly below normal; jerking movements of the arms or legs; mental retardation; seizures and skin rashes.
• Cause: in a healthy baby, phenylalanine is converted into tyrosine by the enzyme phenylalanine hydroxylase. Due to a point mutation, this enzyme becomes defective and converts phenylalanine into toxic phenylketones that accumulate and damage the central nervous system. It is also due to an autosomal recessive gene, and one can get the disease if it is inherited from both parents.
• Treatment: a diet that is extremely low in phenylalanine, particularly when the child is growing. A special infant formula called Lofenalac is made for infants with PKU; it can be used throughout life as a protein source that is extremely low in phenylalanine.

Key terms

Chromatid

One of the two strands of a chromosome; one long, highly coiled DNA molecule with histone proteins.

Centromere (primary constriction)

The point where the two chromatids are attached; it divides the chromosome into two arms.

Secondary constriction (nucleolar organizer)

A second point of union along the chromatids in some chromosomes; it gives rise to nucleoli during interphase.

Telomeres

The terminal ends of chromosomes, which prevent two chromosomes from attaching end to end.

Metacentric, submetacentric, acrocentric, telocentric

Chromosome types with the centromere in the centre, slightly away from the centre, near the end and at the end.

Histone proteins

Positively charged proteins (rich in arginine and lysine) that bind the negatively charged DNA.

Nucleosome

DNA of about 200 nucleotides wrapped twice around a core of eight histones.

Nucleosome string

The 10 nm chain of nucleosomes, 'beads on a string', joined by linker DNA.

Chromatin fibre

The 30 nm fibre formed by further coiling of the nucleosome string; shows heterochromatin and euchromatin.

Heterochromatin

The highly condensed, unexpressed region of the chromatin fibre.

Euchromatin

The non-condensed region of the chromatin fibre whose genes are expressed.

Supercoil

The 300 nm coil formed from the chromatin fibre at the start of cell division.

Transformation

The transfer of genetic material from one organism to another, which alters the genetic make-up of the recipient.

DNA replication

The self-synthesis of a DNA molecule, which occurs once in the S phase.

Semi-conservative model

Each daughter DNA has one parental and one new strand.

Conservative model

One daughter DNA has both parental strands and the other has both new strands.

Dispersive model

The parental DNA is dispersed into nucleotides that combine with new ones in both daughters.

Origin of replication

The specific nucleotide sequence from where replication begins.

Replication bubble and replication fork

The bubble-like opening of DNA at the origin and each side of it where unwinding proceeds.

DNA helicase

The enzyme that opens the DNA duplex by breaking the base pairs.

DNA gyrase

The enzyme that works ahead of helicase and reduces the tension created by unwinding.

Single-stranded binding (SSB) proteins

Proteins that stop the separated DNA strands from pairing again.

Primase and primer

The enzyme that arranges short RNA nucleotides (primers) on the template as the start site for DNA polymerase.

Primosome

The complex of primase and DNA helicase.

DNA polymerase I, II and III

I replaces RNA primers by DNA; II repairs DNA damage; III is the main enzyme that makes both daughter strands.

Leading strand

The daughter strand made continuously towards the replication fork.

Lagging strand and Okazaki fragments

The daughter strand made discontinuously, away from the fork, as short Okazaki fragments.

Proofreading

The ability of a DNA polymerase III subunit to remove a wrongly added nucleotide.

DNA ligase

The enzyme that joins DNA segments by phosphodiester bonds.

Central dogma of molecular genetics

DNA makes protein through an intermediate RNA by transcription and translation.

Gene expression

The flow of genetic information from genes to proteins, genotype to phenotype.

Transcription

The synthesis of RNA from DNA; the first step of gene expression.

Promoter region

The regulatory part of a gene with the binding sites for RNA polymerase.

RNA polymerase (core enzyme, holoenzyme)

The enzyme of transcription; the core enzyme plus the sigma factor is the holoenzyme.

Transcription bubble

The bubble formed where the DNA unwinds as RNA polymerase binds.

Template (antisense) strand and coding (sense) strand

The strand copied into mRNA and the other strand of the gene.

Terminator and GC hairpin

The gene region that stops transcription and the GC-rich loop in the RNA that makes the polymerase stop.

Introns and exons

Non-coding parts removed from the pre-mRNA and the coding parts that are joined.

Cap and poly-A tail

The 7-methyl GTP cap at the 5′ end and the 30 to 500 adenine tail at the 3′ end that protect mRNA.

RNA splicing and spliceosome

The removal of introns and joining of exons, catalysed by the RNA-protein spliceosome.

Genetic code

The relationship between the nucleotide sequence of DNA (mRNA) and the amino acid sequence of a protein.

Codon

A triplet of mRNA bases that specifies one amino acid.

Start codon, stop codon

AUG (methionine) begins a chain; UGA, UAG and UAA end it.

Sense and nonsense codons

Codons that code for an amino acid and the three stop codons that do not.

Degeneracy of the code

One amino acid can be coded by more than one codon.

Translation

The decoding of mRNA by the ribosome into a polypeptide; the second step of gene expression.

Aminoacyl-tRNA complex

An amino acid bound to the 3′ end of its tRNA by aminoacyl-tRNA synthetase.

Initiation complex

Small subunit, mRNA and first aminoacyl-tRNA, completed by the large subunit.

P, A and E sites

The ribosome sites for the peptide bond, for the arriving tRNA and for the exit of empty tRNA.

Translocation

The movement of the ribosome along the mRNA by one codon from 5′ to 3′.

Release factor

The protein that recognizes a stop codon and ends translation.

Differential gene expression

The expression of different genes by cells with the same genome.

Positive and negative gene regulation

Control of expression by an activator or by a repressor.

Operon and lac operon

A cluster of genes for a coordinated function; the lac operon (i, z, y, a) breaks down lactose.

Mutation, mutagen, mutant

A permanent change in DNA; the agent that causes it; the organism that carries it.

Natural and induced mutations

Mutations that occur automatically and those produced artificially.

Point mutation and chromosomal mutation

A change in a few nucleotides and a change in chromosome structure or number.

Frame shift mutation

Insertion or deletion of nucleotides that changes the whole sequence of codons after it.

Down, Klinefelter and Turner syndromes

Chromosomal disorders with 47 (trisomy 21), 47 (44+XXY) and 45 (44+XO) chromosomes.

Sickle cell anaemia and phenylketonuria

Recessive gene mutations affecting haemoglobin and phenylalanine hydroxylase.

FBISE 2025 and 2026 questions

Questions from the FBISE HSSC-I 2026 (1st Annual) and FBISE HSSC-I 2025 (1st Annual) papers that belong to this unit, answered the way an examiner expects.

Exam focus

1. Identify parts A to F of a DNA replication fork and explain each (helicase, primer, polymerase III, leading and lagging strands, Okazaki fragments, ligase). (long)
   Asked in both 2026 papers as the Section C OR (Set B Q.3 OR, 6 marks; Set D Q.3 OR, 6 marks), and the enzymes were asked in 2025 (Set B Q.2 (xii) OR, Set D MCQ 11). Practise labelling a fork from memory.
   Go to answer
2. Meselson and Stahl experiment: procedure, band results and why DNA replication is semi-conservative (with diagram). (long)
   A 7-mark long question in 2025 (Set D Q.3) and an interpretation of the tubes in 2025 (Set B Q.2 (xi) OR); book long question 6.
   Go to answer
3. Translation: initiation complex, the three elongation steps and termination, with diagrams. (long)
   2025 Set B Q.4 (7 marks), 2026 Set B Q.2 (x) OR (elongation steps) and 2026 Set D Q.2 (x) OR (initiation complex); tRNA anticodon in 2025 Set D MCQ 1.
   Go to answer
4. Watson and Crick double helix structure of DNA, with a labelled diagram. (long)
   Section C Q.4 (6 marks) in both 2026 sets. It is taught in unit 2, so revise it with this chapter.
   Go to answer
5. Griffith and Hershey-Chase experiments: controls, conclusions and the finding that DNA is the genetic material. (short)
   2026 MCQ 17 in both sets, Set B Q.2 (iii) OR (Griffith controls) and Set D Q.2 (iii) OR (Hershey-Chase findings); book long questions 3 and 4.
   Go to answer
6. Point mutation and sickle cell anaemia (CTT to CAT, glutamic acid to valine); sources of mutagens. (short)
   2025 Set B Q.2 (vi) OR and 2025 Set D Q.2 (xiv); book long questions 15 and 18.
   Go to answer
7. Types of chromosomes by centromere position. (short)
   2025 Set B MCQ 9 and Set D Q.2 (xii) OR; book exercise MCQ 6 and short question 1.
   Go to answer
8. Transcription and post-transcriptional modification of mRNA (sigma factor, cap, poly-A tail, splicing). (short)
   2025 Set D Q.2 (ii) OR and 2025 Set B MCQ 4 (sigma factor leaves the promoter); book long questions 9 and 14.
   Go to answer
9. Characteristics of the genetic code and the lac operon. (short)
   Not asked in the 2025 and 2026 papers; included from the book's short question 5 and long question 13, and from the unit's learning outcomes on gene regulation.
   Go to answer