Prokaryotes: Biology unit 6 notes (FBISE class 11)

6.1Taxonomy of prokaryotesOften examined

Cells are broadly of two kinds: prokaryotic cells and eukaryotic cells. Prokaryotic cells are simpler in structure. Unlike eukaryotes, prokaryotes lack a membrane-bound nucleus, lack membrane-bound organelles and microtubules, and have simpler flagella.

Kingdom Monera

In 1969 the American biologist Robert H. Whittaker introduced a five-kingdom system that included the basic distinction between prokaryotes and eukaryotes. This system was revised in 1988 by Lynn Margulis and Karlene V. Schwartz, who placed all prokaryotic organisms in one separate kingdom, Monera.

Phylogenetic position of prokaryotes

Phylogenetics: The study of evolutionary relatedness among various groups of organisms (for example species and populations). The word comes from Greek: phyle (tribe, race) and genetikos (relative to birth, from genesis, birth).
Phylogeny (phylogenesis): The origin and evolution of a set of organisms, usually a set of species.

The word "bacteria" traditionally meant all tiny, single-celled prokaryotes. Molecular systematics then showed that prokaryotic life has two distinct domains. They were first named Eubacteria and Archaebacteria but are now called Bacteria and Archaea. These two domains evolved independently from a common ancient ancestor and, together with Eukarya, form the widely accepted three-domain system.

The three-domain system. Bacteria and Archaea are both prokaryotes (kingdom Monera); together with Eukarya they come from an ancient common ancestor.

Milestones in the classification of prokaryotes
Who and when	What they did
Robert H. Whittaker, 1969	Introduced the five-kingdom system, which separated prokaryotes from eukaryotes.
Carl Woese, 1977	Identified that archaea have an evolutionary lineage separate from bacteria. This led to the three-domain system: eubacteria, archaea and eukaryotes.
Lynn Margulis and Karlene V. Schwartz, 1988	Revised the five-kingdom system and named the kingdom Monera for all prokaryotes.

How old are prokaryotes?

The ancestors of present-day bacteria were ancient, single-celled microorganisms that appeared on Earth about 4 billion years ago.
For roughly 3 billion years all life forms stayed microscopic, with bacteria and archaea dominating the biosphere.
The most recent common ancestor of bacteria and archaea lived about 2.5 to 3.2 billion years ago and was probably a hyperthermophile (an organism that lives at very high temperatures).

6.2ArchaeaOften examined

Archaea were first called archaebacteria (from the Greek archaios, meaning ancient). They are prokaryotic cells that live in extreme environments resembling the conditions on early Earth. Later research showed how distinct they are, so they were placed in a separate domain, Archaea.

Unifying features of Archaea (6.2.1)

They have special lipids in their membranes that help them live in very hot or acidic places.
Unlike some other microbes, archaea have no cell walls made of peptidoglycan.
Some archaea make methane, a gas.
Many archaea make their own food using hydrogen, sulphur, carbon dioxide and water.
Although they look like bacteria, they have different genetic and molecular traits, for example their ribosomal RNA.

Table 6.1: Differences between eubacteria and archaea
Main feature	Eubacteria	Archaea
rRNA sequences	Many unique to eubacteria	Many match eukaryotes
RNA polymerase	Relatively small and simple	Complex, similar to eukaryotes
Introns (non-coding parts of genes)	Absent	Present in some genes
Peptidoglycan in cell wall	Present	Absent
Membrane lipids	Carbon chains unbranched	Carbon chains branched

Most archaea inhabit extreme environments

Modern archaea have adapted to many extreme environments, which indicate conditions that were common on early Earth but are not present today. The book describes three groups.

Groups of archaea
Group	Meaning of the name	Where they live	Example
Methanogens	methano, methane; gen, producer (methane producers)	Anaerobic places such as swamps, marshes and the intestinal tracts of humans and other animals	Methanobacterium smithii (present in the human gut)
Halophiles	halo, salt; philes, lover	Salty environments where few other life forms survive, for example heavily salted fish and meat	Holobacterium halobium
Thermoacidophiles	Thrive in hot and acidic conditions	Hot springs, geysers and volcanic areas	Thermoplasma acidophilum and Thermus aquaticus

6.3Bacteria: ecology and diversity

The kingdom Prokaryotae is made up of organisms commonly known as bacteria. The study of bacteria is called bacteriology and is an important branch of microbiology.

Discovery and naming of bacteria
Scientist	Year	Contribution
Anton van Leeuwenhoek (Dutch)	1674	First discovered bacteria, using a single-lens microscope of his own design. He called them "animalcules" and published his observations in a long series of letters to the Royal Society.
Christian Gottfried Ehrenberg	1882	Introduced the name bacterium, from the Greek word bakteria, meaning "little stick".

6.3.1Occurrence of bacteria in the widest range of habitatsOften examined

Eubacteria, a huge group of prokaryotes, are found almost everywhere on the planet. They play a central part in sustaining various life forms, and the existence of nearly all other forms of life depends on them. Certain structural features help eubacteria thrive in a great variety of environments.

Structural features that help bacteria live everywhere

Flagella. Bacteria with flagella can move towards more favourable places or away from less favourable ones. This motility is a vital adaptation that lets bacteria seek the best conditions for growth and reproduction.
Pili. These hair-like structures on the bacterial surface help bacteria stick (adhere) to one another and to various surfaces, such as rocks in flowing streams or the lining of the human intestine. Adhesion is crucial for colonisation, nutrient acquisition and other biological processes.
Endospores. Eubacteria can form endospores, a distinctive survival strategy. In harsh conditions the outer cell may disintegrate, but the endospore survives all sorts of trauma, including lack of water and nutrients, extreme heat or cold and most poisons. When the environment becomes better, the endospore absorbs water and resumes growth.
Branching cell chains or filaments. This feature is unique to the eubacterial group called actinomycetes. They are very common in soil, where they break down organic substances. The filaments let the organism bridge dry gaps between soil particles.

Together these features explain the wide distribution and ecological importance of eubacteria in nature.

Worked example: link each feature to a habitat problem

A bacterium must (a) leave a place that has become unsuitable, (b) stay attached to the wall of a fast-flowing stream, (c) survive a long dry, hot summer, and (d) cross a dry gap between soil particles to reach food. Name the structure that solves each problem and say how.

Problem	Structure	How it solves the problem
(a) Leave an unsuitable place	Flagella	The cell swims towards favourable conditions or away from unfavourable ones.
(b) Stay on rocks in a stream	Pili	These hair-like structures make the bacteria adhere to the surface, so they are not washed away.
(c) Survive heat, drought and poisons	Endospore	The spore withstands lack of water and nutrients, extreme heat or cold and most poisons, then takes in water and grows again when conditions improve.
(d) Cross a dry gap in soil	Branching filaments (actinomycetes)	A chain of cells forms a bridge between soil particles.

Phylogenetic groups of bacteria

Some common phylogenetic groups of bacteria are given in Table 6.2.

Table 6.2: Common phylogenetic groups of bacteria
Bacterial group	Characteristics
Aquificales	Extremely thermophilic bacteria, the oldest branch of the bacterial domain. E.g. Aquifex
Green non-sulphur bacteria	Most bacteria in this group are photosynthetic; some are thermophilic. E.g. Chloroflexus, Thermomicrobium
Green sulphur bacteria	Green phototrophic bacteria that do not produce oxygen during photosynthesis. E.g. Chlorobium
Proteobacteria (purple bacteria)	Gram-negative bacteria. Some are phototrophic but do not produce oxygen during photosynthesis, some are chemotrophic, and some members can fix nitrogen. E.g. Escherichia, Salmonella
Gram-positive bacteria	Includes endospore-forming bacteria, lactic acid bacteria, anaerobic and aerobic cocci and others. E.g. Staphylococcus, Clostridium, Bacillus, Mycoplasma
Cyanobacteria	Phototrophic bacteria that produce oxygen during photosynthesis. E.g. Nostoc, Anabaena, Oscillatoria
Bacteroides	Gram-negative, rod-shaped bacteria. E.g. Bacteroides, Flavobacterium

Diagnostic features of the major groups of bacteria

Historically, bacteria have been divided taxonomically into groups on the basis of their cell wall type (Gram-positive or Gram-negative), presence of endospores, metabolism, growth and nutritional characteristics, physiological characteristics and other criteria.

6.3.2Cyanobacteria: the most prominent photosynthetic bacteriaOften examined

Cyanobacteria (Greek kyanoa, blue, and bacterion, rod) are often called blue-green algae, but they are a type of Gram-negative bacteria.

Habitats and forms of life

They live in damp places, salt water, fresh water, moist soil, rocks in flowing streams, tree trunks and even hot springs with temperatures up to 85 °C.
They can have an epiphytic or symbiotic lifestyle, forming partnerships with organisms such as liverworts, ferns and, at times, invertebrates such as corals. With fungi they form lichens.
They are believed to have been among the first life forms to colonise land during evolution.
They exist in three forms of life: (a) unicellular and solitary, (b) colonies, (c) filaments with cells attached end to end.

Prokaryotic features of cyanobacteria

The nuclear membrane is absent.
The chromosomes have no protein combined with the DNA.
Membrane-bound organelles are absent.
The cell wall contains muramic acid, which is found only in prokaryotes. The wall is often surrounded by a mucilaginous sheath.
The genetic material is a circular strand of DNA.
Many ribosomes are present in the cytoplasm.

Figure 6.1: Cyanobacteria (Anabaena and Nostoc). The thick-walled heterocysts (coloured) are the cells that fix nitrogen.

Photosynthesis in cyanobacteria

Photosynthesis takes place in an extensive system of membranes in the outer zone of the cytoplasm.
Oxygen is released during photosynthesis.
Cyanobacteria use phycobilins as accessory pigments. Phycocyanin, a blue pigment, is the main phycobilin.
They are believed to be the organisms that first introduced oxygen into the primitive atmosphere.

Nitrogen fixation

About one-third of cyanobacteria can fix atmospheric nitrogen, often inside heterocysts: specialised cells with thick walls and no nuclei. In regions like Pakistan, cyanobacteria such as Nostoc and Anabaena are deliberately cultivated to improve soil fertility because they fix nitrogen.

Reproduction

Sexual reproduction is absent in cyanobacteria. Asexual reproduction takes place in four ways.

Asexual reproduction in cyanobacteria
Method	What happens
Cell division	Seen, for example, in the unicellular forms.
Fragmentation	The body breaks into small fragments. It happens at weak points next to a heterocyst. The fragments are called hormogonia.
Formation of akinetes	Certain cells of the filament become enlarged and their walls become thick. They contain reserve food and DNA and are the resting stages. After resting, the wall of the akinete ruptures and a short filament of cells is released.
Spore formation	Not common. Sometimes the heterocyst forms endospores: the nuclear material divides and then the cytoplasm of the heterocyst divides within the parent cell wall, forming many spores. Each spore grows into a new Nostoc filament.

6.4Structure: shape and size of bacteriaOften examined

A typical bacterium consists of a cell wall, a cell membrane, cytoplasm, genetic material and specialised structures outside the cell wall.

Figure 6.1 (b): A typical bacterial cell.

Parts of a bacterial cell
Part	What the book says about it
Cell wall	The outermost component common to all bacteria. It supports the cell and maintains its characteristic shape.
Cell (plasma) membrane	Lies inside the wall. Cell wall is absent in Mycoplasma species, which are bounded only by the cell membrane. In photosynthetic bacteria the pigment (bacteriochlorophyll) is built into the membrane of the mesosomes or is scattered in the cytoplasm.
Cytoplasm	Contains the genetic material (DNA), ribosomes and inclusions.
Genetic material	A single circular chromosome located in the nucleoid region, plus small rings of DNA called plasmids.
Surface structures outside the wall	Capsule, flagella and pili.

The cell wall

The cell wall is a multilayered structure outside the cytoplasmic membrane. It is made of an inner layer of peptidoglycan and an outer membrane that varies in thickness and chemical composition with the type of bacterium. Peptidoglycan gives structural support and maintains the shape of the cell.

Peptidoglycan: A complex interwoven network that surrounds the whole cell. It is one huge macromolecule made of singly covalently linked units and is found only in bacterial cell walls. The name comes from the peptide and the sugars (glycan) that make it up. Synonyms are murein and mucopeptide.
Capsule: A gelatinous layer covering the whole bacterium. It is made of polysaccharide, except in Anthrax bacillus, where it is polymerised D-glutamic acid. The sugars in the polysaccharide differ from one species to another. The capsule may help bacteria stick (adhere) to human tissues.

Figure 6.2: Peptidoglycan. Chains of sugars (S) are cross-linked by short chains of amino acids (AA), forming one interwoven network around the cell.

Worked example: identify the parts

In the diagram of a bacterial cell, five parts are lettered A to E. Name each part and give one function.

Lettered bacterial cell.

Use the position of each part, then say what the book says it does.

Letter	Part	Function
A (outermost jelly-like layer)	Capsule	Gelatinous layer of polysaccharide that may help the cell adhere to human tissues.
B (thick layer outside the membrane)	Cell wall	Supports the cell and keeps its shape (peptidoglycan).
C (coiled thread in the centre)	Bacterial (chromosomal) DNA in the nucleoid	Carries the genetic information; a single circular molecule.
D (small separate ring)	Plasmid	Accessory ring of DNA; can be passed to another cell in conjugation.
E (long thread leaving the cell)	Flagellum	Rotates and moves the cell towards or away from stimuli.

6.4.1Cell walls of Gram-positive and Gram-negative bacteriaOften examined

The cell wall maintains the structural integrity of bacteria and protects them from their external environment. The two major groups, Gram-positive and Gram-negative bacteria, differ fundamentally in the composition and structure of their cell walls.

Gram-positive bacteria

A notably thicker peptidoglycan layer than Gram-negative bacteria.
Some also have fibres of teichoic acid that protrude outside the peptidoglycan layer. This feature is absent in Gram-negative bacteria.

Gram-negative bacteria

A multifaceted outer layer (outer membrane) made of lipopolysaccharides, lipoproteins and phospholipids.
Between this outer membrane and the cytoplasmic membrane lies the periplasmic space.
In some species the periplasmic space is the site of enzymes called beta-lactamases ( $β$ -lactamases). They break down penicillin and other $β$ -lactam drugs, and so contribute to antibiotic resistance in Gram-negative bacteria.

Figure 6.3: Cell wall of bacteria. Gram-positive bacteria have a thick peptidoglycan layer with teichoic acids; Gram-negative bacteria have a thin peptidoglycan layer between the periplasm and an outer membrane.

Gram-positive and Gram-negative cell walls compared
Feature	Gram-positive	Gram-negative
Peptidoglycan layer	Thick	Thin
Teichoic acid fibres	Present in some	Absent
Outer membrane (lipopolysaccharides, lipoproteins, phospholipids)	Absent	Present
Periplasmic space	Not shown in the book's figure	Present, between the outer membrane and the cytoplasmic membrane
Enzymes that break down penicillin ( $β$ -lactamases)	Not mentioned	In the periplasm of specific species

Worked example: explain why

Some Gram-negative bacteria are not killed by penicillin. Using the structure of their cell wall, explain why.

Answer in four steps

Locate the layers. A Gram-negative wall has an outer membrane (lipopolysaccharides, lipoproteins, phospholipids) outside a thin peptidoglycan layer. Between the outer membrane and the cytoplasmic membrane is the periplasmic space.
Identify the key feature. In specific species the periplasmic space contains the enzymes called $β$ -lactamases.
Link to the drug. Penicillin is a $β$ -lactam drug, and $β$ -lactamases break down penicillin and other $β$ -lactam drugs before they can act.
Conclude. The bacteria are therefore resistant to the antibiotic, so the drug does not kill them.

6.4Diversity of shapes and sizes in bacteriaOften examined

Bacteria have three main shapes: spherical, rod-shaped and spiral.

Figure 6.4: Forms of bacteria. Round cells are cocci, rods are bacilli and spiral cells are spirochetes; the way the cells stay together gives the arrangement names.

Shapes of bacteria
Shape	Arrangement or form	Description
Spherical (coccus, plural cocci)	Diplococci	Groups of two cells
Spherical	Streptococci	Long chains of cells
Spherical	Staphylococci	Irregular clumps that look like bunches of grapes
Spherical	Tetrad	Packet of 4 cells
Spherical	Octate (sarcina)	Packet of 8 cells
Rod-shaped (bacilli)	Diplobacillus	Pairs of rods
Rod-shaped	Coccobacilli	Very short, ovoid rods
Rod-shaped	Vibrio	Curved into a form like a comma
Rod-shaped	Palisade	Rods that look like a stack of coins
Spiral	Spirochetes	Thin-walled, flexible spiral rods that usually occur singly and seldom form colonies; relatively large and flexible

Examples of cocci: Streptococcus pneumoniae, Neisseria meningitidis.
Examples of rod-shaped bacteria: Escherichia coli, Pseudomonas.
Example of a spirochete: Treponema pallidum.

Size of bacteria. Bacteria range in size from about 0.1 to 600 $μ$ m in a single dimension.

6.4.2Endospore formation in bacteriaOften examined

Endospore formation, or sporulation, is a process in which a single bacterium forms a single spore. The spore contains bacterial DNA, a small amount of cytoplasm, ribosomes, peptidoglycan, very little water and, most importantly, a thick, keratin-like coat. Because the spore develops inside the vegetative cell it is called an endospore.

Endospore formation lets bacteria such as Clostridium and Bacillus endure extreme conditions, including high temperatures, desiccation (drying) and exposure to chemicals. When conditions become favourable again, the endospores germinate and give rise to active vegetative cells capable of growth and reproduction.

Stages of endospore formation

Initiation. Bacteria meet unfavourable conditions such as shortage of nutrients or extreme temperatures and begin sporulation. DNA replicates, giving two identical copies.
Asymmetric division. The bacterium divides unequally, giving a larger mother cell and a smaller forespore, which will develop into the endospore.
Membrane development. Several protective membranes form around the forespore, shielding its genetic material and essential parts.
Peptidoglycan layer. The mother cell makes layers of peptidoglycan around the forespore, forming the core of the endospore.
Spore coat formation. The mother cell produces a protein spore coat that adds an extra layer of protection.
Maturation. The endospore dehydrates, so its water content falls greatly.
Release. Finally the mother cell ruptures and releases the mature endospore into the environment, where it stays dormant until conditions improve.

The seven stages of sporulation, drawn from the book's list: the spore forms inside the cell (hence endospore) and is released when the mother cell ruptures.

Figure 6.5: Endospore. A vegetative cell makes a spore by sporulation; the spore turns into a germinated cell by germination and grows into a vegetative cell again.

Figure 6.5 labels these parts of the spore: spore coat, outer membrane, cortex, spore wall, inner membrane and core. The core holds the bacterial DNA, a little cytoplasm and ribosomes, with very little water.

Worked example: explain why

Explain why endospore formation is called a survival mechanism and not reproduction.

Process	Starting number of cells	Number of cells at the end	Purpose
Endospore formation (sporulation and germination)	1 vegetative cell	1 spore, then 1 vegetative cell: no increase	Survival through harsh conditions
Binary fission	1 cell	2 daughter cells	Reproduction (increase in number)

Define reproduction: it increases the number of individuals.
Count the cells in sporulation. A single bacterium forms a single spore; when it germinates it gives a single active cell. The number never rises.
State what the spore does achieve. The thick coat, low water content and extra membranes let the cell survive heat, desiccation, chemicals and lack of nutrients until conditions improve.
Conclude: sporulation is survival (a resting stage), not reproduction.

6.4.3Motility in bacteriaOften examined

Motile bacteria can move in several ways: using flagella, bacterial gliding, twitching motility or by changes of buoyancy.

Spirochetes have structures similar to flagella. They have a distinctive helical body that twists about as it moves.
In twitching motility bacteria use their pili like a grappling hook: the pilus is repeatedly extended, anchored and then retracted with remarkable force.

Arrangement of flagella

Bacterial species differ in the number and arrangement of flagella on their surface.

Flagellar arrangements
Term	Arrangement of flagella
Monotrichous	A single flagellum
Amphitrichous	A flagellum at each end of the cell
Lophotrichous	Clusters (tufts) of flagella at the poles of the cell
Peritrichous	Flagella distributed over the entire surface of the cell

Figure 6.6: Location of flagella in bacteria.

Swimming, tumbling and taxes

Many bacteria, such as E. coli, have two distinct modes of movement: forward movement (swimming) and tumbling. Tumbling lets them reorient themselves, which makes their movement a three-dimensional random walk.

Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes. They include chemotaxis, phototaxis and magnetotaxis. Several species move inside host cells by taking over the host's cytoskeleton, which is normally used to move organelles inside the cell.

Taxis (plural taxes): Movement of a motile bacterium towards or away from a stimulus.
Chemotaxis, phototaxis, magnetotaxis: Taxis in response to chemicals, light and magnetic fields respectively.

6.4.4Structure of bacterial flagellumOften examined

Many bacteria have fine, thread-like outgrowths called flagella (singular: flagellum). A flagellum is made of a single protein, flagellin, arranged in intertwined chains. These proteins are non-contractile and there are no microtubules. Flagella are about 20 nanometres in diameter and up to 20 micrometres long.

Figure 6.7: Structure of a bacterial flagellum: basal body, hook and filament.

The three parts of a bacterial flagellum
Part	Description and function
Basal body	Originates just beneath the cell membrane. A complex structure that produces rotatory motion.
Hook	Connects the basal body to the filament.
Filament	A hollow structure made of several protein chains twisted into a helical structure.

The 360 degree rotation of the flagellum makes the cell spin and move forward.

6.4.5Genomic organization in bacteriaOften examined

The genetic material of a typical bacterium, Escherichia coli, is a single circular DNA molecule of about $5 \times 1 0^{6}$ base pairs. This amount of genetic information can code for about 2000 proteins.

Bacterial genome: one large circular chromosome and, in many bacteria, small plasmid rings. (Drawn from the text; sizes not to scale.)

Most bacteria have a single circular chromosome. Its size ranges from only about 160,000 base pairs in the endosymbiotic bacterium Candidatus Carsonella ruddii to about 12,200,000 base pairs in the soil-dwelling bacterium Sorangium cellulosum.
The spirochetes of the genus Borrelia are a notable exception: they contain a single linear chromosome.
Apart from the chromosome, many bacteria have accessory rings of DNA called plasmids.
According to the book, eight complete bacterial genomes had been sequenced to date.

Plasmid: An accessory ring of DNA found in many bacteria in addition to the main chromosome. (A plasmid is what is transferred in bacterial conjugation.)
Nucleoid: The region of the cell where the single, circular bacterial chromosome is located (there is no nucleus).

6.5.1Autotrophic nutrition in bacteriaOften examined

Bacteria can be classified on the basis of how they obtain energy and carbon. Carbon metabolism in bacteria is either heterotrophic, where organic carbon compounds are used as the carbon source, or autotrophic, where cellular carbon is obtained by fixing carbon dioxide.

Modes of nutrition in bacteria. Autotrophs fix carbon dioxide; heterotrophs use organic carbon compounds.

Autotrophy means self-nourishing. An autotrophic organism can obtain all the carbon it needs from carbon dioxide, which is present in the atmosphere and dissolves readily in water. There are two major groups of autotrophs: photosynthetic and chemoautotrophic bacteria.

Photosynthetic bacteria

They contain a special type of chlorophyll called bacteriochlorophyll, built into the membrane of their mesosomes or scattered in the cytoplasm.
Like green plants, they use the energy of sunlight to make carbohydrates from carbon dioxide.
They use hydrogen sulphide ( $H X_{2} S$ ) instead of water as the hydrogen source, so sulphur (not oxygen) is released.
Examples: green sulphur bacteria, purple sulphur bacteria, purple non-sulphur bacteria.

2 H X_{2} S + CO X_{2} light chlorophyll (CH X_{2} O) X_{n} + H X_{2} O + 2 S

Photosynthesis in sulphur bacteria

Chemoautotrophic bacteria

Certain colourless bacteria make carbohydrates from inorganic substances. They do not use light energy.
They oxidise inorganic substances, and the energy released by this oxidation is then used to make carbohydrates. Sulphur bacteria, for example, oxidise sulphur compounds to produce energy.
Examples: nitrifying bacteria and sulphur bacteria.

2 H X_{2} S + O X_{2} 2 S + 2 H X_{2} O + energy

Step 1: energy from oxidation of hydrogen sulphide

2 H X_{2} S + CO X_{2} energy (CH X_{2} O) X_{n} + H X_{2} O + 2 S

Step 2: the energy is used to make carbohydrate

Photosynthetic and chemoautotrophic bacteria compared
Feature	Photosynthetic bacteria	Chemoautotrophic bacteria
Source of energy	Sunlight (light energy)	Energy released by oxidising inorganic substances
Source of carbon	Carbon dioxide	Carbon dioxide
Pigment	Bacteriochlorophyll present	Colourless bacteria, no light-trapping pigment mentioned
Examples	Green sulphur, purple sulphur and purple non-sulphur bacteria	Nitrifying bacteria, sulphur bacteria

6.5.2Heterotrophic nutrition in bacteriaOften examined

Heterotrophic bacteria depend on external organic sources to obtain carbon and energy. They cannot fix carbon dioxide from the atmosphere. Instead they take complex organic molecules, such as sugars and proteins, as their main source of carbon and energy. Many bacteria with different lifestyles, including those in soil, the human digestive system and water, are heterotrophic. There are two types: saprotrophic and parasitic.

Saprotrophic bacteria

They obtain nutrition from dead organic matter, such as decaying plants, animals and other organic debris.
They secrete extracellular enzymes that break down complex organic substances into simpler molecules, which the bacteria then absorb.
By decomposing organic materials they release essential nutrients back into the environment, which supports the ecosystem.
Examples: Pseudomonas, Azobacter.

Parasitic nutrition

Parasitic bacteria obtain nutrients and energy from host organisms. They are typically pathogenic and can cause various diseases in their hosts. They have developed special mechanisms, such as toxins and virulence factors, to enter host tissues, escape the host's immune system and secure nutrients for their own growth and reproduction. Their lifestyle often harms or damages the host.

Parasitic bacteria
Type of parasite	Meaning	Example
Obligate parasite	Depends completely on the host to complete its life cycle	Rickettsia (causes disease)
Facultative parasite	Not dependent on the host to complete its life cycle; can survive independently without the host	Escherichia coli

Some common parasitic bacteria are Streptococcus pneumoniae, Salmonella typhi, Mycobacterium tuberculosis and Vibrio cholerae.

Respiration in bacteria (book box)

Respiration may be aerobic or anaerobic, so bacteria are grouped according to their need for oxygen.

Bacteria and oxygen
Group	Oxygen requirement	Example
Aerobic bacteria	Need oxygen	Pseudomonas
Anaerobic bacteria	Grow without oxygen	Spirochaeta
Facultative bacteria	Grow either in the presence or absence of oxygen	E. coli
Microaerophilic bacteria	Need a low concentration of oxygen for growth	Campylobacter

Autotrophy and heterotrophy compared
Feature	Autotrophy	Heterotrophy
Carbon source	Carbon dioxide (inorganic)	Organic carbon compounds such as sugars and proteins
Ability to fix carbon dioxide	Present	Absent
Energy source	Light (photosynthetic) or oxidation of inorganic substances (chemoautotrophic)	The organic compounds taken from outside
Types	Photosynthetic and chemoautotrophic	Saprotrophic and parasitic
Examples	Green and purple sulphur bacteria; nitrifying bacteria	Pseudomonas, Azobacter (saprotrophs); Vibrio cholerae (parasite)

6.5.2Difference between the photosynthesis mechanism in cyanobacteria and other photosynthetic bacteriaOften examined

Cyanobacteria have a more complex photosynthetic apparatus, produce oxygen and use a wider range of pigments to absorb light than other photosynthetic bacteria. Other photosynthetic bacteria have adapted to particular ecological niches with their own pigment systems and do not add significantly to atmospheric oxygen.

Photosynthesis in cyanobacteria and other photosynthetic bacteria
Feature	Cyanobacteria (blue-green algae)	Other photosynthetic bacteria (purple and green bacteria)
Photosynthetic pigments	A diverse array: chlorophyll a, chlorophyll b and phycobiliproteins (phycocyanin and phycoerythrin)	Purple bacteria use bacteriochlorophylls; green sulphur bacteria use chlorosomes containing bacteriochlorophyll c and other pigments
Light absorbed	A broad spectrum, including blue and red wavelengths	Mainly infrared and near-infrared regions
Where it happens	In thylakoids, membrane-bound structures arranged in stacks called grana, like the chloroplasts of plant cells	Pigments are embedded in the cell membrane, forming infoldings called chromatophores; no thylakoids
Oxygen production	Oxygen is produced; during the light-dependent reactions water molecules are split and oxygen is released as a by-product, as in plants	Most do not produce oxygen; they often use sulphur compounds or other molecules as electron donors
Habitat note	Wide range of habitats	Often in anaerobic environments with limited exposure to visible light

6.6Growth and reproduction in bacteriaOften examined

Bacteria reproduce by binary fission. Because one cell gives rise to two progeny cells, bacteria undergo exponential growth (logarithmic growth).

Exponential growth by binary fission
Generation	0	1	2	3	4
Number of cells	1	2	4	8	16
As a power of 2	$2^{0}$	$2^{1}$	$2^{2}$	$2^{3}$	$2^{4}$

Exponential growth by binary fission
Generation	Number of cells	As a power of 2
0	1	$2^{0}$
1	2	$2^{1}$
2	4	$2^{2}$
3	8	$2^{3}$
4	16	$2^{4}$

Thus one bacterium will produce 16 bacteria after four generations. Each generation multiplies the number of cells by 2.

Generation (doubling) time: The time taken for a population of bacteria to double in number.

Growth of one bacterium by binary fission

20

40

60

80

100

120

10

20

30

40

50

60

70

O

Time (minutes)

Cells

2

8

32

64

Cells

The number of cells doubles every generation (here every 20 minutes), so the curve rises faster and faster.

Worked example: counting cells by doubling

One E. coli cell divides every 20 minutes and nothing limits growth. How many cells are present after 80 minutes? How many generations and how much time are needed to reach 64 cells?

Find the number of generations in 80 minutes. Each generation takes one doubling time of 20 minutes.
$\frac{80 min}{20 min} = 4 generations$
Double the number of cells once for each generation, as in the book's series $1, 2, 4, 8, 16$ ( $2^{0}$ to $2^{4}$ ).
$1 \to 2 \to 4 \to 8 \to 16$
For 64 cells keep doubling: $16 \to 32 \to 64$ takes two more generations, so six generations in all.
$6 \times 20 min = 120 min$

Check by doubling
Time (min)	0	20	40	60	80	100	120
Generation	0	1	2	3	4	5	6
Cells	1	2	4	8	16	32	64

Check by doubling
Time (min)	Generation	Cells
0	0	1
20	1	2
40	2	4
60	3	8
80	4	16
100	5	32
120	6	64

16 cells after 80 min; 64 cells after 6 generations (120 min)

The same growth with the logarithm of the number

20

40

60

80

100

120

0.5

1

1.5

2

O

Time (minutes)

lo g_{10} N

lo g_{10} N

Plotting the logarithm of the number against time gives a straight line, which is why the log phase is a straight line on the growth curve.

6.6.1Phases of growthOften examined

The growth curve is called a logarithmic or exponential curve. Such curves can be turned into straight lines by plotting the logarithm of growth against time. The growth cycle of bacteria has four major phases.

Typical growth curve of a bacterial population

Figure 6.8: Typical growth curve of a bacterial population (\log_{10}N is the logarithm of the number of living bacteria).

The four phases of bacterial growth
Phase	What happens	Why
Lag phase (no growth)	Bacteria adapt to their new environment; growth has not yet reached its maximum rate	They may be synthesising new enzymes to digest the particular nutrients available in the new medium
Log phase (rapid growth)	Growth proceeds at its maximum rate, closely approaching a logarithmic increase in numbers; the growth curve is a straight line	Conditions are favourable and cells divide repeatedly
Stationary phase (death rate equals reproduction rate)	Growth rate is zero; there is much greater competition for resources. New cells are produced more slowly and may stop; any increase is offset by deaths, so the number of living cells stays constant	Exhaustion of essential nutrients, accumulation of toxic waste products of metabolism and, for aerobic bacteria, possibly depletion of oxygen
Death (decline) phase (bacteria start dying)	The death rate increases and cells stop multiplying	Final phase of the cycle

Skills: performing and recording

The book asks you to draw a graph presenting the time taken in each phase of bacterial growth and the number of bacteria.

Phases of growth (*Escherichia coli*)
Phase	Time taken in phases	Number of bacteria
Lag phase	10 minutes	1
Log phase	180 minutes	1000
Stationary phase	180 to 360 minutes	3000
Death phase	360 to 1800 minutes	300

Skills activity: phases of growth of Escherichia coli

The data of the book's table plotted against time (minutes). The stationary phase has the largest number; the death phase falls to 300.

6.6.2Reproduction in bacteriaOften examined

The two types of reproduction in bacteria are asexual reproduction and sexual reproduction.

Asexual reproduction: binary fission

The main method of asexual reproduction in bacteria is binary fission.

Steps of binary fission

DNA replication. Before the cell divides it copies its genetic material. Bacterial DNA is usually a single circular chromosome in the nucleoid region. Replication begins at the origin of replication and goes in both directions (bidirectionally), giving two identical DNA molecules.
Elongation of the cell. As DNA replication goes on, the cell grows longer by adding new cell wall and membrane material continuously. This makes enough cell components to share between the two daughter cells.
Cell division. Once DNA replication is complete and the cell is long enough, the plasma membrane pinches inward at the midpoint (it invaginates), making two compartments. A septum (cross wall) forms and separates the two daughter cells.
Formation of daughter cells. The result is two genetically identical daughter cells. Each has its own complete set of cell components, including a copy of the chromosome, and is able to grow and metabolise on its own.

Figure 6.9: Binary fission in bacteria.

Binary fission is a rapid and efficient method of reproduction. It allows bacteria to adapt quickly to changing environments and to multiply in favourable conditions, so bacterial populations can increase exponentially. Examples of bacteria that reproduce by binary fission include Escherichia coli and Staphylococcus aureus.

Sexual reproduction: genetic recombination

Sexual reproduction in bacteria is genetic recombination: the DNA of two bacteria combines to give a new type of bacterium called a recombinant. Genetic recombination in bacteria occurs by conjugation, transduction and transformation.

Conjugation

For a long time people believed that bacteria simply split in two and that all bacteria of a kind were the same. In 1946 Joshua Lederberg and Edward Tatum showed that bacteria can exchange genes in a way similar to sexual reproduction in more complex organisms. They found that bacteria can share DNA through a bridge-like connection and were awarded a Nobel Prize for this and other work.

Experiment of Lederberg and Tatum

The experiment

They took wild type Escherichia coli, which could make all the substances needed for growth and reproduction when grown on a minimal medium containing inorganic salts and glucose.
They irradiated the wild type with X-rays to cause mutations. They selected two types of mutant: one that could not make substance A, and another that needed substance B in the minimal medium to grow.
Both mutant types were grown in a nutrient medium containing both A and B.
After a period of growth three types of bacteria were obtained: (a) like one parent, unable to make A; (b) like the other parent, unable to make B; (c) like the wild type, able to grow in the minimal medium without A and B.
Conclusion: the offspring of the two mutant types were wild type, which is possible only when actual genetic recombination takes place.

The Lederberg and Tatum experiment (1946), drawn from the book's description. The wild-type offspring show that genes were exchanged.

Figure 6.10: Sexual reproduction in bacteria by forming a conjugation bridge. The plasmid (coloured) is copied and passed from donor to recipient.

6.6.3Direct proof of genetic recombinationOften examined

With the invention of the electron microscope the direct proof of genetic recombination was obtained. A mixture of two mutants was observed with the electron microscope; the mutants are easily told apart by their structure. The bacterium that gives the DNA is the donor and the bacterium that receives it is the recipient.

Bacterial conjugation involves a plasmid that can be transferred from donor to recipient during the process. In some cases, however, a part of the bacterial chromosomal genes is also transferred.

Transduction

Transduction is a genetic transfer process in bacteria that is carried out by bacteriophages, which are viruses that infect bacterial cells. During infection phages inject their genetic material into bacteria.

Figure 6.11: Generalised transduction by a bacteriophage. The bacterial DNA that is carried from one cell to another is coloured.

Transformation

When bacteria die, or when they are reproducing very rapidly, they release fragments of their DNA into their immediate environment. Transformation is the absorption of DNA into a cell, so that the cell is changed into a new type of cell. These cells are called transformed cells. Bacterial cells that release DNA fragments are called donor cells. If one of the released fragments touches a cell of a species that is capable of transformation, the fragment may bind to the recipient and be taken inside.

Conjugation, transduction and transformation compared
Feature	Conjugation	Transduction	Transformation
How DNA is carried	Directly from cell to cell through a bridge-like connection	By a bacteriophage (a virus that infects bacteria) that injects genetic material into the bacterium	Free DNA fragments in the surroundings are absorbed (taken up) by the cell
Contact between cells	Needed (donor and recipient)	Not needed; the phage is the carrier	Not needed; DNA comes from dead or rapidly reproducing cells
Material transferred	Usually a plasmid; sometimes part of the chromosomal genes	Genes of the bacterium packaged in new phages	DNA fragments released by donor cells
Result	Recipient receives plasmid DNA (a recombinant)	New host DNA includes bacterial genes brought by the phage	Recipient becomes a transformed cell

Mutations and genetic recombination in bacteria

Bacteria, as asexual organisms, inherit identical copies of their parents' genes (they are clonal). Yet all bacteria can evolve by selection on changes to their genetic material, DNA, caused by genetic recombination or by mutations. Mutations come from errors made in the replication of DNA or from exposure to mutagens.

Mutation rates vary widely among different species of bacteria and even among different clones of a single species.
Genetic changes in bacterial genomes come either from random mutation during replication or from "stress-directed mutation", where genes involved in a growth-limiting process have an increased mutation rate.

Worked example: which gene-transfer process?

Identify the process of genetic recombination in each case and give a reason. (a) A harmless bacterium takes up a fragment of DNA released by a dead cell lying nearby and changes into a new type. (b) A virus that infects bacteria injects its DNA into a cell, and later new virus particles carrying some bacterial DNA infect another cell. (c) A plasmid is copied and passed through a bridge-like connection from one cell to another cell.

Case	Process	Reason
(a)	Transformation	The cell absorbs free DNA fragments from its surroundings and is changed into a transformed cell.
(b)	Transduction	A bacteriophage carries genetic material between cells; the new phages carry some bacterial DNA to the next host.
(c)	Conjugation	DNA (a plasmid) passes from donor to recipient through a bridge-like connection.

6.7 and 6.7.1Nutrients recyclingOften examined

Bacteria are useful as recyclers of nature, and they also have ecological as well as economic importance.

Bacteria play a vital part in recycling nutrients, which makes them essential for nutrient cycles such as the nitrogen cycle.

Bacteria in the nitrogen cycle

Nitrogen fixation. Within the root nodules of legumes, nitrogen-fixing bacilli of the genus Rhizobium change nitrogen gas into ammonium.
Breakdown of waste. Saprotrophic soil bacteria break down nitrogenous waste from animals and plants, forming ammonia.
Nitrification. Chemosynthetic bacteria, Nitrosomonas and Nitrobacter, convert ammonia into nitrate.
Denitrification. Denitrifying bacteria convert nitrates into nitrogen gas again.

The part of the nitrogen cycle done by bacteria, drawn from the book's description.

Roles of bacteria in the nitrogen cycle
Process	Bacteria	Change
Nitrogen fixation	Rhizobium (nitrogen-fixing bacilli in root nodules of legumes)	Nitrogen gas to ammonium
Breakdown of nitrogenous waste	Saprotrophic soil bacteria	Nitrogenous waste to ammonia
Nitrification	Nitrosomonas and Nitrobacter (chemosynthetic)	Ammonia to nitrate
Denitrification	Denitrifying bacteria	Nitrate to nitrogen gas

Bacteria recycle both organic and inorganic substances, including minerals, water, ammonia and carbon dioxide. Through fermentation bacteria release carbon dioxide into the atmosphere, which green plants later take up and use.

6.7.2Ecological importance of bacteria

Bacteria and fungi are nature's decomposers. They have the special task of breaking down dead plants and animals. Through their metabolic processes the organic material of these once-living things is changed into humus.

Humus enriches the soil with essential nutrients.
Humus also improves the ability of the soil to retain moisture.
This contributes greatly to the health and productivity of ecosystems.

6.7.3Economic importance of bacteriaOften examined

Bacteria are both beneficial and harmful. This section covers the beneficial side, including their use in research and technology; the harmful side follows in the next sections.

Beneficial bacteria

Beneficial roles of bacteria
Benefit	What bacteria do
Help in digestion	Bacteria in the intestines play a crucial part in digestion. Some species help emulsify fats in food, making it easier for the host to digest and absorb them. In animals such as cattle, certain bacteria break down complex substances like cellulose and starch.
Synthesis of vitamins	Specific bacteria make essential vitamins, including vitamin K and vitamin B12. Escherichia coli is one such bacterium. The vitamins have both commercial and nutritional importance.
Bacteria in industry	Industries use bacteria to make products cheaply and efficiently: acetic acid (used in vinegar production), acetone, lactic acid, butanol (a type of alcohol), vitamins, cheese and tobacco flavourings. Bacteria also take part in the coffee and leather (tanning) industries.
Bacteria in the food industry	Bacteria are pivotal in making dairy products: yogurt, cheese and butter are made with the help of specific strains of bacteria.
Nutrient source	Partially digested plant material carries a large number of bacterial cells through the digestive tracts of animals. The bacteria are digested themselves and give the host animal a significant part of its amino acids and vitamins.
Antibiotics	A large proportion of antibiotics used in medicine come from bacteria: streptomycin, auromycin, tetramycin and many others are very effective against bacterial infections. Most antibiotics are obtained from various species of actinomycetes.
Biogas	Bacteria decompose organic waste such as sewage, dung, garbage and even stool. During this decomposition they make methane gas, a valuable fuel. Biogas plants in many villages use this methane (typically 54 to 70 percent methane) as an energy source.
Single cell protein	A recent addition to the food industry: protein obtained from the large-scale cultivation of microorganisms such as bacteria, yeast, fungi and algae. It can be used for human food or animal feed, a sustainable way to produce protein.

Use of bacteria in research

Microorganisms such as bacteria, yeast and Neurospora have been used extensively in research. We owe many biological achievements to bacteria. For example, in 1952 Alfred D. Hershey and Martha Chase used T2 bacteriophage and bacteria to prove that DNA is the hereditary material.

Use of bacteria in technology

Free-living organisms that have a foreign gene inserted into them are called transgenic organisms.

Bacteria in technology
Use	What it means
Biotechnology products	Bacteria are used to clone a gene or to mass-produce a product. Products include hormones, other proteins and vaccines, for example insulin, growth hormones and clotting factor VII for haemophilia.
Protection and enhancement of plants	Genetically engineered bacteria can protect plant health. For example, bacteria that normally live on plants and encourage ice crystals to form have been changed from "frost-plus" to "frost-minus" bacteria.
Bioremediation	Naturally occurring bacteria that eat oil can be genetically engineered to clean up beaches after oil spills.
Chemical production	Organic chemicals are often made with bacteria carrying out the synthesis. It is now possible to manipulate the genes that code for these enzymes; for example, genetically engineered bacteria are used to make phenylalanine.
Mineral processing	Genetic engineering may improve the ability of bacteria to extract copper, uranium and gold from low-grade sources.

6.7.4Harmful bacteria

Bacteria produce acids that convert wine to vinegar.
Bacteria cause decay of wood, leather, fabrics and similar materials.
Bacteria spoil food materials by decomposition.
Parasitic bacteria attack plants and cause various diseases in them.
Many human diseases are also caused by bacteria.

Bacteria cause many diseases in man, such as pneumonia, anthrax, tetanus, botulism, diphtheria, meningitis, gonorrhoea, whooping cough, plague, urinary tract infection, typhoid fever, gastritis, peptic ulcer, cholera, tuberculosis and syphilis. The book discusses only cholera, typhoid, tuberculosis and pneumonia in detail.

6.7.4Important bacterial diseases in manOften examined

Cholera, typhoid, tuberculosis and pneumonia are described with their symptoms, causative agent, treatment and prevention (SLO 19).

Cholera

Symptoms: Profuse watery diarrhoea.
Causative agent: The bacterium Vibrio cholerae.
Treatment: Timely and sufficient replacement of fluids and electrolytes, by mouth or into a vein (intravenously). Antibiotics such as tetracycline are not mandatory but can shorten the duration of symptoms and the time during which the organisms are excreted.
Prevention: Mainly public health measures that ensure a clean water supply. A vaccine of killed organisms has limited usefulness; a live vaccine is available in certain countries. Tetracycline is effective for prevention. Prompt detection of carriers is important in limiting outbreaks.

Typhoid

Symptoms: Typhoid and other enteric (intestinal) fever infections begin in the small intestine. The onset is slow, with fever and constipation. High fever, delirium, tender abdomen and enlarged spleen occur. "Rosy spots" (rose-coloured macules on the abdomen) are associated with typhoid fever but occur rarely.
Causative agent: The bacterium Salmonella typhi.
Treatment: Antibiotics should be used in patients who are chronic carriers of S. typhi.
Prevention: Mainly public health and personal hygiene: hand washing before food handling, pasteurisation of milk and proper cooking of poultry, eggs and meat. Vaccines are available.

Tuberculosis (pulmonary TB)

Symptoms: In primary tuberculosis: mild fever for 7 to 14 days and mild dry cough; bluish-red raised tender lesions of the skin on the shins and, less commonly, on the thighs. In secondary tuberculosis: low-grade intermittent fever (usually in the evening), night sweats, weight loss, anorexia, malaise and weakness, dry hacking cough with blood-stained sputum, and dull ache in the chest due to pleurisy.
Causative agent: The bacterium Mycobacterium tuberculosis.
Treatment: Multiple-drug therapy is used to prevent drug-resistant mutants during the long 6 to 9 month treatment, or DOTS (directly observed treatment short course) of only two months.
Prevention: Prompt identification and adequate treatment of patients who are coughing up the organism. Masks and respiratory isolation procedures protect medical staff. A vaccine containing a strain of live Mycobacterium bovis (Bacillus Calmette-Guerin, BCG) can give partial resistance.

Pneumonia

Symptoms: Often begins with sudden chills, cough and pleuritic pain. The sputum is red-brown, "rusty" in colour.
Causative agent: The bacterium Streptococcus pneumoniae.
Treatment: Most pneumococci are susceptible to penicillin and erythromycin.

The book gives no prevention for pneumonia.

Summary of the four diseases
Disease	Causative agent	Key symptom	Main prevention
Cholera	Vibrio cholerae	Profuse watery diarrhoea	Clean water supply
Typhoid	Salmonella typhi	Slow onset fever with constipation; rosy spots (rare)	Hand washing, pasteurised milk, well-cooked food, vaccine
Tuberculosis	Mycobacterium tuberculosis	Dry hacking cough with blood-stained sputum, night sweats, weight loss	Treat patients promptly; masks; BCG vaccine
Pneumonia	Streptococcus pneumoniae	Sudden chills, cough, pleuritic pain, rusty sputum	Not given in the book

6.7.4Important bacterial diseases in plantsOften examined

The important bacterial diseases of plants are leaf spots, blights, soft rots, wilts and galls (SLO 20).

Leaf spot

Symptoms: The most common symptoms are discrete or spreading lesions on the leaf blade. They are caused by toxins that the bacterial pathogens produce.
Cause: Xanthomonas campestris on tomato and pepper; Pseudomonas syringae on tobacco; Aplanobacter sepedanium causes ring disease of potato.
Prevention: Prevent contact between the pathogen and the host; use disease-free seeds.

Blight

Symptoms: When necrotic (dead-tissue) symptoms develop very rapidly, they damage the plant cell wall structure and affect an organ or shoot, or the whole plant is soon killed. This is called blight. Often the symptoms start at or near the leaf tip or margin and spread downwards and inwards, drying up the leaf; the whole plant may soon be blighted, for example maize, rice and oat.
Cause: Xanthomonas oryzae causes blight in rice; Erwinia amylovora causes fire blight of pears and apples.
Prevention: Disease-free seeds, a suitable location and removal of the diseased plant by a physical method.

Soft rot

Symptoms: Plant tissue cells die because of the action of the pathogen, which produces pectolytic and cellulolytic enzymes. Rotting may affect any organ of a plant, including flowers and fruits. The plant cells separate from one another (maceration), the host tissue loses its coherence and water leaks from the affected cells, which die. The dead tissue becomes wet to the touch and soft, hence "soft rot". It spreads fast and damages plant organs very rapidly.
Cause: Erwinia atroseptica in potato; Corynebacterium causes ear rot of wheat.
Prevention: Removal of diseased plants by a physical method.

Wilting

Symptoms: The upward transport of water with dissolved nutrients from the roots through the stem to the leaves is interfered with. The leaf blade loses turgidity and becomes limp. This loss of turgidity increases with time and ends in wilting and drying of the leaf.
Cause: Pseudomonas solanacearum causes wilt disease of potato; Xanthomonas campestris causes important wilt diseases.
Prevention: Selecting disease-free seeds, choosing proper dates for planting and a suitable location, and allowing proper spacing between plants.

Galls

Symptoms: Localised outgrowths, mostly small but very large in some diseases.
Cause: Rhizobium leguminosarum causes small galls called root nodules in legumes. Pseudomonas savastonoi causes a small gall in the olive plant known as olive knot. Agrobacterium tumefaciens causes large galls in many plants. Xanthomonas campestris causes galls on cotton.
Prevention: Crop rotation, removal of diseased plants and use of disease-free seeds.

Bacterial diseases of plants at a glance
Disease	Symptom in one line	Example of cause
Leaf spot	Discrete or spreading lesions on the leaf blade	Xanthomonas campestris (tomato, pepper)
Blight	Very rapid death of leaf, shoot or whole plant	Xanthomonas oryzae (rice)
Soft rot	Wet, soft, rotting tissue	Erwinia atroseptica (potato)
Wilt	Loss of turgidity, leaves limp and dry	Pseudomonas solanacearum (potato)
Gall	Localised outgrowth	Agrobacterium tumefaciens (many plants)

6.8The bacterial flora of humansOften examined

There are about ten times as many bacterial cells as human cells in the human body, with large numbers of bacteria on the skin and in the digestive tract.

Normal flora: The various bacteria (and fungi) that are permanent residents of certain body parts, especially the skin, oropharynx, colon and vagina.

Table 6.3: Some members of the normal flora and their locations
Member of the normal flora	Anatomical location
Clostridium species	Colon
Escherichia coli and other coliforms	Colon, vagina, outer urethra
Lactobacillus species	Mouth, colon, vagina
Staphylococcus aureus	Nose, skin
Enterococcus faecalis	Colon
Viridans streptococci	Mouth, nasopharynx

Benefits of the bacterial flora to humans

Benefits of the bacterial flora
Benefit	How the flora helps
Digestive health	Gut flora help digestion and the absorption of nutrients. They break down complex carbohydrates and make essential vitamins such as B vitamins and vitamin K.
Immune system support	Beneficial bacteria help stimulate the immune system, making it more resilient against harmful pathogens, and help regulate the immune response, preventing excessive inflammation.
Protection against pathogens	The microbiota is a protective barrier that stops harmful bacteria colonising the gut. This competitive exclusion keeps a healthy balance.
Synthesis of beneficial compounds	Gut bacteria make short-chain fatty acids (SCFAs) such as butyrate, which have anti-inflammatory and metabolic benefits.
Mood and brain health	Emerging research suggests a link between the gut microbiome and mental health; some gut bacteria may influence mood and behaviour through the gut-brain axis.
Vaginal health	Lactobacilli in the vaginal microbiota maintain an acidic environment, which prevents overgrowth of harmful bacteria and yeast infections.
Detoxification	Gut bacteria can help metabolise and detoxify certain compounds.
Metabolism and weight regulation	The make-up of the gut microbiome may play a part in metabolism and weight management.
Development of the immune system	Exposure to microbes early in life helps shape the developing immune system, possibly reducing the risk of allergies and autoimmune diseases.
Protection against antibiotic-associated problems	Beneficial bacteria help restore balance in the gut after antibiotic treatment, reducing the risk of antibiotic-associated diarrhoea and infections.
Synthesis of essential nutrients	Some gut bacteria help make essential nutrients such as biotin and folate.
Maintaining homeostasis	The microbiota contributes to the overall balance and stability of various body systems, promoting health and well-being.

6.9Chemical methods to control bacteriaOften examined

Chemical methods are important in healthcare, food production and sanitation. They use chemical agents to inhibit the growth of bacteria or kill them.

Chemical methods to control bacteria
Chemical method	What it is and where it is used	Examples
1. Disinfectants	Chemicals that kill or inhibit bacteria on surfaces and inanimate objects. Common in hospitals, laboratories and households	Bleach (sodium hypochlorite), hydrogen peroxide, quaternary ammonium compounds
2. Antiseptics	Like disinfectants but made for use on living tissues such as skin and mucous membranes, to prevent or treat bacterial infections	Alcohol-based hand sanitisers, iodine-based antiseptics, hydrogen peroxide
3. Preservatives	Added to food and cosmetic products to inhibit the growth of bacteria and other microorganisms, making the product last longer	Sodium benzoate, potassium sorbate, parabens
4. Chemical agents in water treatment	Used in water treatment plants to disinfect drinking water and control bacterial growth in water distribution systems	Chlorine and chloramine
5. Chemotherapy	The use of chemicals to treat bacterial infections; often used when antibiotics are ineffective	Sulphonamides, nitrofurans

6.9Physical methods to control bacteriaOften examined

Physical agents such as heat, radiation, filtration and cold are also used to control bacteria.

Physical methods to control bacteria
Physical method	What it does	Notes and examples
Sterilisation	Uses physical agents such as steam, dry heat, gas, filtration and radiation to control bacteria. It is destructive to all life forms	Used to sterilise surgical instruments; also on a large scale to preserve foods such as milk and meat
High temperature	Both dry and moist heat are used in microbiology laboratories	Moist heat causes protein coagulation and microbial death; dry heat causes oxidation of microbial parts, which kills them
Radiation	Certain electromagnetic radiations, especially those below 300 nm, kill microorganisms	Gamma rays are commonly used for sterilisation
Membrane filter	Heat-sensitive compounds such as antibiotics and sera can be sterilised using membrane filters	Keeps them pure and safe
Pasteurisation	Introduced by Louis Pasteur: controlled heating to kill non-spore-forming bacteria	Milk at 71 °C for 15 seconds, or 62 °C for about 30 minutes; keeps the taste of the product and reduces the risk of diseases such as typhoid and tuberculosis
Low temperature	Food is preserved by storing it at 10 to 15 °C, which extends shelf life	Milk, vegetables, cheese, meat
Freezing	Food keeps for weeks to months at -10 to -18 °C	Meat and vegetables
Drying (dehydration)	Removing water prevents bacterial growth in foods	Dried milk and dried meat

Activity 6.1STEAM activity: bacterial growth and antibiotic sensitivity

Activity 6.1: Bacterial growth and antibiotic sensitivity. The materials needed are agar plates, sterile cotton swabs, nutrient broth and some common antibiotics. Bacterial samples can be taken from students' hands, surfaces and so on.

Procedure

Prepare agar plates by pouring nutrient broth agar into petri dishes and letting it set. Divide each plate into sections.
Inoculate the agar plates with the collected bacterial samples, using the swabs. Each section can represent a different sample source.
Apply different antibiotics to each section of the plate.
Incubate the plates for a few days and observe bacterial growth. Record the size of the bacterial colonies and note how effective the antibiotics are.
Present your findings to the class.

This activity introduces the important issue of antibiotic resistance and helps develop an understanding of responsible antibiotic use.

Formula sheet

Photosynthesis in sulphur bacteria (book equation, corrected)

\ce{2H2S + CO2 ->[light][chlorophyll] (CH2O)_n + H2O + 2S}

Hydrogen sulphide, not water, is the hydrogen source, so sulphur is released instead of oxygen.

Energy from oxidation of hydrogen sulphide by chemoautotrophic bacteria

\ce{2H2S + O2 -> 2S + 2H2O + energy}

The energy released is then used to build carbohydrate from carbon dioxide.

Carbohydrate synthesis using the energy of oxidation

\ce{2H2S + CO2 ->[energy] (CH2O)_n + H2O + 2S}

Chemoautotrophic bacteria fix carbon dioxide using chemical energy, not light.

Key terms

Prokaryote: A cell that has no membrane-bound nucleus, no membrane-bound organelles and no microtubules, and has simpler flagella.
Monera: The kingdom proposed by Margulis and Schwartz (1988) for all prokaryotic organisms.
Phylogenetics: The study of evolutionary relatedness among various groups of organisms.
Phylogeny: The origin and evolution of a set of organisms, usually a set of species.
Archaea: The domain of prokaryotes (once called archaebacteria) that live mostly in extreme environments, have no peptidoglycan in the cell wall and have branched membrane lipids.
Eubacteria: The domain of 'true' bacteria, now called Bacteria; their cell walls contain peptidoglycan.
Methanogens: Archaea that make methane and live in anaerobic places such as swamps, marshes and the intestines of animals.
Halophiles: Archaea that live in very salty environments.
Thermoacidophiles: Archaea that thrive in hot and acidic conditions such as hot springs, geysers and volcanic areas.
Bacteriology: The study of bacteria; an important branch of microbiology.
Actinomycetes: Eubacteria with branching cell chains or filaments, common in soil; most antibiotics are obtained from them.
Cyanobacteria: Gram-negative, oxygen-producing photosynthetic bacteria (blue-green algae) that use phycobilins as accessory pigments.
Phycocyanin: The blue pigment that is the main phycobilin of cyanobacteria.
Heterocyst: A thick-walled cell without a nucleus in which cyanobacteria fix atmospheric nitrogen.
Akinete: A thick-walled, enlarged cell of a cyanobacterial filament that stores food and DNA and serves as a resting stage.
Hormogonia: Short fragments of a cyanobacterial filament that form by fragmentation next to a heterocyst.
Peptidoglycan: A network of sugars and short peptides forming a single covalently linked macromolecule found only in bacterial cell walls; also called murein or mucopeptide.
Capsule: A gelatinous layer outside the cell wall, usually of polysaccharide, that may help bacteria adhere to tissues.
Gram-positive bacteria: Bacteria with a thick peptidoglycan layer, and in some cases teichoic acid fibres.
Gram-negative bacteria: Bacteria with a thin peptidoglycan layer and an outer membrane of lipopolysaccharides, lipoproteins and phospholipids, with a periplasmic space.
Periplasmic space: The space between the outer membrane and the cytoplasmic membrane of Gram-negative bacteria; it can contain beta-lactamases.
Beta-lactamases: Enzymes in the periplasm of some Gram-negative bacteria that break down penicillin and other beta-lactam drugs, causing antibiotic resistance.
Coccus: A spherical bacterium (plural cocci).
Bacillus: A rod-shaped bacterium (plural bacilli).
Spirochete: A thin-walled, flexible, spiral bacterium that usually occurs singly.
Endospore: A resistant spore formed inside a bacterial cell by sporulation, with a thick protein coat, little water and the bacterial DNA.
Sporulation: Endospore formation: the process in which one bacterium forms one spore; it is a survival mechanism, not reproduction.
Flagellum: A thin protein thread of a bacterium made of flagellin, with a basal body, hook and filament, that rotates to move the cell.
Monotrichous: Having a single flagellum.
Amphitrichous: Having a flagellum at each end of the cell.
Lophotrichous: Having clusters of flagella at the poles of the cell.
Peritrichous: Having flagella distributed over the whole surface of the cell.
Taxis: The attraction or repulsion of motile bacteria by a stimulus, for example chemotaxis, phototaxis and magnetotaxis.
Plasmid: An accessory ring of DNA in a bacterium, in addition to the chromosome.
Nucleoid: The region of a bacterial cell where the single circular chromosome lies.
Autotrophic: Obtaining carbon by fixing carbon dioxide (self-nourishing).
Heterotrophic: Obtaining carbon and energy from organic compounds.
Photosynthetic bacteria: Autotrophic bacteria with bacteriochlorophyll that use light energy to make carbohydrates from carbon dioxide.
Chemoautotrophic bacteria: Colourless autotrophic bacteria that make carbohydrates using energy from oxidising inorganic substances.
Saprotrophic bacteria: Heterotrophic bacteria that feed on dead organic matter using extracellular enzymes.
Parasitic bacteria: Heterotrophic bacteria that obtain nutrients from a host and often harm it; they may be obligate or facultative.
Aerobic and anaerobic bacteria: Bacteria that need oxygen (aerobic) or grow without it (anaerobic); facultative bacteria grow with or without oxygen and microaerophilic bacteria need a low oxygen concentration.
Chromatophores: Infoldings of the cell membrane that carry photosynthetic pigments in purple and green bacteria.
Binary fission: Asexual reproduction in which one bacterial cell divides into two genetically identical daughter cells.
Generation (doubling) time: The time for a bacterial population to double in number.
Lag phase: The first phase of growth, in which bacteria adapt to the new medium and growth has not reached its maximum rate.
Log phase: The phase of fastest, exponential growth.
Stationary phase: The phase in which births equal deaths and the number of living cells stays constant.
Death phase: The final phase of growth, in which the death rate increases and cells stop multiplying.
Recombinant: A new type of bacterium formed when DNA from two bacteria combines.
Conjugation: Transfer of DNA, usually a plasmid, from a donor to a recipient bacterium through a bridge-like connection.
Transduction: Transfer of bacterial genes from one bacterium to another by a bacteriophage.
Transformation: Absorption of free DNA fragments from the surroundings into a bacterial cell, changing it into a transformed cell.
Mutation: A change in the DNA of a bacterium caused by errors in replication or by mutagens.
Nitrification: Conversion of ammonia into nitrate by Nitrosomonas and Nitrobacter.
Denitrification: Conversion of nitrate into nitrogen gas by denitrifying bacteria.
Normal flora: The bacteria (and fungi) that are permanent residents of certain body parts such as the skin, oropharynx, colon and vagina.
Pasteurisation: Controlled heating (for example milk at 71 °C for 15 seconds) that kills non-spore-forming bacteria.

Multiple choice questionsp. 174–175

1

What distinguishes cyanobacteria from other types of bacteria in terms of photosynthesis?

AThey lack photosynthetic pigments.
BThey perform photosynthesis using chlorophyll.Answer
CThey rely on chemosynthesis for energy.
DThey are not involved in any form of photosynthesis.

Why

Cyanobacteria are photosynthetic: they carry chlorophyll-a with phycobilin pigments and release oxygen (p.152, p.160). A is wrong because they do have pigments; C describes chemosynthetic bacteria, which oxidize inorganic substances and need no light; D is wrong because cyanobacteria do photosynthesize.

Note. Of the four options only B is true, but other photosynthetic bacteria also use chlorophyll-type pigments. The feature unique to cyanobacteria, release of oxygen from water, is not offered; B is the key by elimination.

2

What is the primary pigment responsible for photosynthesis in cyanobacteria?

AChlorophyllAnswer
BCarotenoids
CPhycobilins
DXanthophylls

Why

Chlorophyll-a is the main photosynthetic pigment of cyanobacteria. Phycobilins (phycocyanin and phycoerythrin) are only accessory pigments: they absorb other wavelengths and pass the energy on (p.152). Phycobilins are the tempting wrong answer because the book names them first in the pigment discussion.

Note. The book (p.160) lists chlorophyll-a and chlorophyll-b among the pigments of cyanobacteria. Chlorophyll-a is the one the answer relies on.

3

Pili are made up of pilin, which is:

AA type of lipid
BA proteinAnswer
CA nucleic acid
DA carbohydrate

Why

Pilin is a protein. Pili are hair-like surface structures that let bacteria adhere to one another and to surfaces (p.158). Lipid, nucleic acid and carbohydrate are not the building blocks of pili, although bacterial membranes are made of lipids and the wall of a sugar-peptide polymer.

4

What is the primary characteristic of pathogenic bacteria?

AThey are beneficial to the host.
BThey cause diseases in their hosts.Answer
CThey only exist in extreme environments.
DThey are essential for nitrogen fixation.

Why

A pathogen is a bacterium that causes disease in its host. The book describes parasitic bacteria as pathogenic (p.160). A describes beneficial bacteria, C describes extremophiles such as archaea, and D describes nitrogen-fixing bacteria such as Rhizobium.

5

How do chemosynthetic bacteria obtain energy for growth and metabolism?

AThrough photosynthesis
BBy consuming organic matter
CBy oxidizing inorganic compoundsAnswer
DFrom sunlight

Why

Chemosynthetic (chemoautotrophic) bacteria oxidize inorganic substances, such as hydrogen sulphide, and use the energy released to make carbohydrate from \ce{CO2} (p.159). They do not use light (D) or photosynthesis (A). Consuming organic matter (B) is the way heterotrophs obtain energy.

6

Which pigment is primarily responsible for the purple colour in purple bacteria?

AChlorophyllAnswer
BPhycocyanin
CRhodopsin
DBacteriorhodopsin

Why

Purple bacteria photosynthesize with bacteriochlorophylls, which are chlorophyll-type pigments (p.161). Of the options, chlorophyll is the closest. Phycocyanin is the blue pigment of cyanobacteria (p.152). Rhodopsin and bacteriorhodopsin are light-sensitive protein pigments and are not the photosynthetic pigments that the book gives for purple bacteria.

Note. The book names bacteriochlorophylls for purple bacteria (p.161), and no option gives that name. The key is the nearest option. Bacteriorhodopsin is the purple pigment of archaea, not of the book's purple photosynthetic bacteria, so it is not the intended answer.

7

How are peritrichous flagella arranged on a bacterial cell?

AThey are clustered at one pole of the cell.
BThey are found in a single bundle at the centre of the cell.
CThey are absent in peritrichous bacteria.
DThey are evenly distributed over the entire cell surface.Answer

Why

Peritrichous bacteria have flagella distributed over the entire surface (Fig 6.6). A describes the lophotrichous arrangement (clusters at the poles), B has no matching group in the book, and C is wrong because the name itself refers to flagella.

8

During bacterial conjugation, what specific type of genetic material is typically transferred between two bacterial cells?

APlasmidsAnswer
BExons
CIntrons
DPromoters

Why

In conjugation a plasmid is copied and passed from donor to recipient through a bridge (p.164). Exons and introns are parts of eukaryotic genes, and promoters are regulatory regions; the book notes that introns are absent in eubacteria (Table 6.1).

9

What is a significant difference between bacterial membranes and eukaryotic cell membranes?

ABacterial membranes contain cholesterol.
BEukaryotic membranes have peptidoglycan layers.
CBacterial membranes have a phospholipid bilayer.Answer
DEukaryotic membranes lack membrane proteins.

Why

Bacterial membranes are phospholipid bilayers, as are eukaryotic membranes, so C is the only true statement, although it describes both and is not a difference. A is false because bacterial membranes do not contain cholesterol as a rule. B is false because peptidoglycan forms the bacterial cell wall, not eukaryotic membranes. D is false because membranes carry proteins.

Note. No option is a difference that the book states. C is the only correct statement, so it is keyed, but the question wording is loose.

10

Why are tetanus bacteria resistant to conventional methods of heat treatment, requiring prolonged heating at temperatures significantly above boiling to kill them?

AThey have a unique heat-resistant outer membrane.
BThey have a thick, protective cell wall.
CThey possess specialized enzymes that protect them from heat.
DThey form spores that are highly heat resistant.Answer

Why

The tetanus bacterium belongs to Clostridium, the genus that forms endospores (p.157). An endospore has a thick coat, little water and dehydrated contents, so it survives boiling and needs prolonged heating. A, B and C do not explain the resistance: a thick wall or special enzymes would not protect a vegetative cell from heat in this way.

Note. The book names tetanus among bacterial diseases (p.169) but does not state its genus; the link to Clostridium is the standard one.

Short answer questionsp. 175–176

13 marks

Write the pigment composition of cyanobacteria.

Solution

Cyanobacteria contain three groups of pigments:

Chlorophyll-a, the main photosynthetic pigment (chlorophyll-b is also listed by the book).
Phycobilins, the accessory pigments, in the form of phycobiliproteins.
Phycocyanin, a blue pigment and the predominant phycobilin, together with phycoerythrin, which helps to capture red wavelengths of light.

23 marks

Do you know the differences between bacteria and archaea?

Solution

Archaea and bacteria are prokaryotes that belong to different domains. Their differences (Table 6.1) are:

Main feature	Eubacteria (bacteria)	Archaea
Cell wall	Contains peptidoglycan	No peptidoglycan
Membrane lipids	Carbon chains unbranched	Carbon chains branched
RNA polymerase	Relatively small and simple	Complex, similar to eukaryotes
Introns in genes	Absent	Present in some genes
rRNA sequences	Many unique to eubacteria	Many match eukaryotes

Archaea also live in extreme environments (methanogens, halophiles and thermoacidophiles), which is typical of the early Earth.

33 marks

What are the morphological forms of bacteria?

Solution

Bacteria have three main shapes:

Spherical (cocci): diplococci (pairs), streptococci (long chains), staphylococci (irregular clumps like grapes), tetrads (groups of four) and octads or sarcinae (packets of eight).
Rod-shaped (bacilli): diplobacilli (pairs), coccobacilli (very short and ovoid), vibrios (curved like a comma) and palisades (stacked like coins).
Spiral: spirochaetes, thin-walled flexible spiral rods that usually occur singly, for example Treponema pallidum.

4

Give the functions of following in bacteria.

Solution

(i) ribosomes

Ribosomes are scattered through the cytoplasm and are the sites of protein synthesis, where amino acids are linked into polypeptides.

(ii) cell membrane

The cell (plasma) membrane is a phospholipid bilayer that controls the entry and exit of substances. In photosynthetic bacteria it carries the pigments in its folds (mesosomes).

(iii) nucleoid

The nucleoid is the region of the cytoplasm that holds the single circular chromosome of DNA. The chromosome is replicated there before binary fission (p.162).

(iv) plasmid

Plasmids are small, accessory rings of DNA that carry extra genes outside the chromosome. They replicate on their own and can be transferred to another bacterium during conjugation (Fig 6.10).

(v) mesosomes

Mesosomes are infoldings of the cytoplasmic membrane. They increase the membrane surface that carries the photosynthetic pigments (chlorophyll is located in their membranes, p.161) and the enzymes of respiration.

(vi) slime capsule

The capsule is a gelatinous polysaccharide layer covering the whole bacterium. It helps bacteria adhere to surfaces and human tissues and protects the cell from its surroundings (p.154).

(vii) flagella

Flagella are protein filaments (flagellin) driven by a basal body. Their 360 degree rotation spins the cell and moves it forward, which gives motility (p.158).

(viii) cell wall

The cell wall is the outermost layer common to bacteria (absent in Mycoplasma). Made of peptidoglycan, it gives structural support and maintains the characteristic shape of the cell (p.154).

(ix) pili

Pili are hair-like surface structures, made of pilin, that help bacteria adhere to one another, to rocks and to the lining of the human intestine. In twitching motility they act as grappling hooks (p.158).

53 marks

How the mechanism of photosynthesis in cyanobacteria is similar and different from that of plants?

Solution

Similarities. Both are oxygenic: water is split in the light-dependent reactions and oxygen is released. Both use chlorophyll-a, capture light in membranes (thylakoids), and use the energy to fix \ce{CO2} into carbohydrate.

Differences.

Feature	Cyanobacteria	Green plants
Cell type	Prokaryotic, no nucleus	Eukaryotic, with a nucleus
Site of thylakoids	Membranes lie free in the cytoplasm	Thylakoids are enclosed in chloroplasts
Accessory pigments	Phycobilins (phycocyanin, phycoerythrin)	Chlorophyll-b and carotenoids
Organelles	No membrane-bound organelles	Chloroplasts and other organelles

63 marks

Draw and label structure of flagellum.

Solution

A bacterial flagellum has three parts: a basal body anchored in the cell envelope and producing rotary motion, a short curved hook that connects the basal body to the filament, and a long hollow filament made of protein chains twisted into a helix (Fig 6.7).

Figure 6.7: Structure of a bacterial flagellum: the basal body is anchored in the plasma membrane, the hook bends the flagellum outward and the hollow filament rotates to move the cell.

73 marks

How chemosynthetic bacteria are autotrophic in nature?

Solution

They take their carbon from carbon dioxide in air or water, not from organic food, so they are autotrophic.
They gain energy by oxidizing inorganic substances, such as hydrogen sulphide to sulphur (sulphur bacteria) or ammonia (nitrifying bacteria). They need no light.
The energy from oxidation is used to fix carbon dioxide into carbohydrate.

\ce{2H2S + CO2 ->[energy] (CH2O)_n + H2O + 2S}

82026 Annual I, Set D, Q.2 (vi) OR2025 Annual I, Set D, Q.2 (iv) OR3 marks

Which chemical methods are used to control microbes?

Solution

Disinfectants: kill or inhibit bacteria on inanimate surfaces, such as bleach (sodium hypochlorite), hydrogen peroxide and quaternary ammonium compounds.
Antiseptics: used on living tissue such as skin and mucous membranes, for example alcohol-based hand sanitizers, iodine-based antiseptics and hydrogen peroxide.
Preservatives: inhibit bacteria in food and cosmetics, for example sodium benzoate, potassium sorbate and parabens. Chlorine and chloramine are used to disinfect water, and chemotherapy uses drugs such as sulphonamides or nitrofurans against infections.

92026 Annual I, Set B, Q.2 (vi) OR2025 Annual I, Set B, Q.2 (ii) OR3 marks

Give physical methods to control microbes?

Solution

Heat: moist heat (steam and pasteurization) coagulates proteins; dry heat oxidizes the constituents of the microbe. Milk is pasteurized at 71^\circ\mathrm{C} for 15 seconds.
Radiation: electromagnetic radiation below 300 nm, such as gamma rays, kills microbes and is used for sterilization.
Filtration: a membrane filter removes microbes from heat-sensitive liquids such as antibiotics and serums.

Low temperature (refrigeration at 10 to 15^\circ\mathrm{C}), freezing (-10 to -18^\circ\mathrm{C}) and drying also control microbes, mainly in food preservation.

103 marks

Name any two bacteria that cause diseases in plants.

Solution

Xanthomonas campestris: leaf spots of tomato and pepper, wilt diseases and galls on cotton.
Pseudomonas solanacearum: wilt disease of potato (p.170).

113 marks

Name any five diseases caused by bacteria in man.

Solution

Pneumonia, caused by Streptococcus pneumoniae.
Tuberculosis, caused by Mycobacterium tuberculosis.
Typhoid fever, caused by Salmonella typhi.
Cholera, caused by Vibrio cholerae.
Diphtheria (from the book's list of bacterial diseases in man, p.168).

Note. The book gives causative agents only for the four diseases it discusses (cholera, typhoid, tuberculosis and pneumonia).

123 marks

Define the term normal flora.

Solution

Normal flora is the term for the various bacteria (and fungi) that are permanent residents of certain body parts, especially the skin, oropharynx, colon and vagina (p.171).

They live on the body all the time rather than being picked up occasionally.
They are harmless residents and many of them are beneficial to the host.
They are named by the body part they live on, for example the flora of the colon or of the skin.

133 marks

What is chemical composition of cell wall of bacteria?

Solution

Peptidoglycan: the main macromolecule, a network of sugar chains (glycan), including muramic acid, cross-linked by short chains of amino acids (peptides). It is also called murein or mucopeptide.
Gram-positive walls: a thick peptidoglycan layer; some species also have teichoic acid fibres that extend outside it.
Gram-negative walls: a thin peptidoglycan layer under an outer membrane made of lipopolysaccharides, lipoproteins and phospholipids.

14

Distinguish between:

Solution

(a) Lysosome and mesosome

Feature	Lysosome	Mesosome
Found in	Eukaryotic cells	Bacteria
Structure	Membrane-bound sac of digestive enzymes	Infolding of the cytoplasmic membrane
Function	Intracellular digestion	Carries photosynthetic pigments and respiratory enzymes

(b) Peptidoglycan and muramic acid

Peptidoglycan is the whole macromolecule that forms the bacterial cell wall: sugar chains (glycan) cross-linked by peptides. Muramic acid is only one of the sugar units inside it. Muramic acid is found only in prokaryotes (p.154), so its presence identifies a bacterial wall.

(c) Gram-positive and Gram-negative bacteria

Feature	Gram-positive	Gram-negative
Peptidoglycan layer	Thick	Thin
Outer membrane	Absent	Present (lipopolysaccharide, lipoprotein, phospholipid)
Teichoic acid	Present in some species	Absent
Periplasmic space	Absent	Present, with \beta-lactamase enzymes

(d) Lytic and lysogenic bacteria

These describe the two ways a bacteriophage infects a bacterium (Fig 6.11). In the lytic cycle the phage DNA takes over the cell, new phages are made and the cell bursts. In the lysogenic cycle the phage DNA (a prophage) is built into the bacterial chromosome and is copied with it until it becomes lytic.

(e) Pathogenic and non-pathogenic bacteria

Pathogenic bacteria cause disease in their hosts, for example Vibrio cholerae and Salmonella typhi. Non-pathogenic bacteria live without causing disease: saprotrophs in soil and water, and the normal flora of the body, many of which are beneficial.

(f) Autotrophy and heterotrophy

Feature	Autotrophy	Heterotrophy
Carbon source	Carbon dioxide	Organic carbon compounds
Energy source	Light or oxidation of inorganic substances	Organic food from the environment or a host
Examples	Photosynthetic and chemosynthetic bacteria	Saprotrophic and parasitic bacteria

(g) Photosynthetic and chemosynthetic bacteria

Feature	Photosynthetic bacteria	Chemosynthetic bacteria
Energy	Sunlight	Energy from oxidizing inorganic substances
Pigments	Bacteriochlorophylls or chlorophyll	No photosynthetic pigments needed
Examples	Green and purple sulphur bacteria	Nitrifying and sulphur bacteria

(h) Mutation and mutant

A mutation is a change in the DNA sequence, caused by errors in replication or by mutagens. A mutant is the cell or organism that carries the mutation and shows a changed trait, such as the E. coli mutants that cannot make substance A (p.164).

(i) Chromosome and a bacteriophage

A chromosome is the single circular DNA molecule of a living bacterium, held in the nucleoid. A bacteriophage is a virus that infects bacteria: it is not a cell, cannot reproduce by itself and injects its DNA into the host.

(j) Bacteria and mitochondria

Bacteria are whole, independent prokaryotic cells without membrane-bound organelles. Mitochondria are organelles inside eukaryotic cells, bounded by a double membrane, which make most of the cell's ATP by respiration.

(k) Prokaryotes and eukaryotes

Feature	Prokaryotes	Eukaryotes
Nucleus	Absent	Present
Membrane-bound organelles	Absent	Present
Microtubules	Absent	Present
Flagella	Simpler, made of flagellin	Made of microtubules

(l) Cyanobacteria and bacteria

Cyanobacteria are a group within the bacteria. They are photosynthetic, produce oxygen like plants, have phycobilin pigments and are Gram-negative (p.152). Most other bacteria are not oxygen-producing photosynthesizers.

Note. The book does not state the Gram-positive versus Gram-negative differences in one place; the table draws them from pp.154 to 155. Item (d) uses the book's phrase 'lytic and lysogenic bacteria' for the two cycles of the phage.

153 marks

What are plasmids?

Solution

Plasmids are small, circular rings of DNA that lie outside the single bacterial chromosome (accessory rings of DNA, p.158).
They carry genes in addition to those on the chromosome.
They replicate independently and can be transferred from one bacterium to another during conjugation (Fig 6.10).

162025 Annual I, Set B, Q.2 (iii) OR3 marks

How do bacteria survive under unfavorable conditions?

Solution

Endospore formation (Bacillus and Clostridium): the bacterium forms a spore with its DNA, little water, peptidoglycan layers and a thick, keratin-like coat. The spore survives high temperatures, dryness, chemicals and lack of nutrients.
Dormancy and release: the spore stays dormant until the mother cell ruptures and releases it into the environment (p.157).
Germination: when conditions improve, the endospore takes up water and grows into an active vegetative cell. Cyanobacteria similarly form thick-walled resting cells (akinetes).

173 marks

List five ways in which bacteria are beneficial to man?

Solution

Digestion: gut bacteria help to digest food and absorb nutrients; in cattle, bacteria break down cellulose and starch.
Vitamins: bacteria such as E. coli synthesize vitamin K and vitamin B12 in the gut.
Food industry: specific strains are used to make yogurt, cheese and butter.
Antibiotics: streptomycin, auromycin and tetramycin are derived from bacteria, mostly actinomycetes.
Biogas: bacteria decompose sewage, dung and garbage to produce methane (54 to 70 per cent of the biogas) used as a fuel.

183 marks

Why are cyanobacteria considered as the most prominent of the photosynthetic bacteria?

Solution

They produce oxygen during photosynthesis, as plants do. The book credits them with introducing oxygen into the primitive atmosphere, while most other photosynthetic bacteria produce none.
They have a more complex photosynthetic apparatus with a wider range of pigments (chlorophyll-a and phycobilins such as phycocyanin and phycoerythrin), so they absorb more of the light spectrum, including blue and red.
They live in the widest range of habitats, from hot springs at up to 85^\circ\mathrm{C} to freshwater, saltwater and moist soil, and about one-third of them fix atmospheric nitrogen in heterocysts.

193 marks

What are the benefits of bacterial flora to human?

Solution

Digestive health: gut bacteria break down complex carbohydrates, aid the absorption of nutrients and produce B vitamins and vitamin K.
Immune system support: beneficial bacteria stimulate the immune system, help regulate the immune response and prevent excessive inflammation.
Protection against pathogens: the normal flora forms a protective barrier and prevents harmful bacteria from settling in the gut (competitive exclusion).
Other health roles: lactobacilli keep the vagina acidic and prevent overgrowth of harmful bacteria and yeast; gut bacteria synthesize biotin and folate.

203 marks

What is the primary function of the F factor in bacterial cells?

Solution

The F (fertility) factor is a plasmid, and its primary function is to allow DNA transfer by conjugation:

It carries the genes for building the conjugation bridge (through which the donor and recipient cells link).
It is copied during conjugation, so that a copy passes through the bridge into the recipient cell.
The recipient receives the plasmid and the genes it carries, which makes the recombination of genetic material possible (Lederberg and Tatum, p.164).

Note. The book does not name the F factor. The answer follows the book's account of conjugation, in which a plasmid is transferred from donor to recipient (p.164).

Extensive answer questionsp. 176

18 marks

Explore the taxonomic and phylogenetic position of prokaryotes.

Solution

Taxonomic position

Rank	Position of prokaryotes
Domains	Bacteria and Archaea (the three-domain system: Bacteria, Archaea and Eukarya)
Kingdom	Monera (Margulis and Schwartz, 1988), also called Prokaryotae in the book
Basis	Prokaryotic cells lack a membrane-bound nucleus, membrane-bound organelles and microtubules, and have simpler flagella (p.148)

Whittaker's five-kingdom system (1969) first separated prokaryotes from eukaryotes. Margulis and Schwartz later named the prokaryotic kingdom Monera.

Phylogenetic position

Phylogenetics is the study of evolutionary relatedness among groups of organisms, and phylogeny is their origin and evolution. Molecular systematics showed that the old group 'bacteria' contains two distinct domains, Bacteria and Archaea. In 1977 Carl Woese found that archaea have a separate evolutionary lineage, which led to the three-domain system: Eubacteria, Archaea and Eukaryota.

Prokaryotes emerged about 4 billion years ago as single-celled microorganisms.
For roughly 3 billion years all life was microscopic, and bacteria and archaea dominated the biosphere.
The most recent common ancestor of bacteria and archaea lived 2.5 to 3.2 billion years ago and was probably a hyperthermophile.
The three domains evolved independently from a common ancestor.

The three-domain system. Bacteria and Archaea are prokaryotes, and the most recent common ancestor of the two lived 2.5 to 3.2 billion years ago. The prokaryotic domains are highlighted.

Conclusion

Prokaryotes occupy their own kingdom Monera, but phylogenetically they fall into two domains. Their position reflects their simple structure and their early evolutionary origin.

28 marks

Rationalize the universal presence of bacteria across diverse habitats.

Solution

Bacteria are found almost everywhere because their structure, metabolism and reproduction let them survive in very different conditions.

Structural features

Flagella let motile bacteria move towards favourable places and away from unfavourable ones.
Pili make bacteria adhere to one another, to rocks in flowing streams and to the lining of the human intestine.
Endospores survive extreme heat or cold, dryness, chemicals and lack of nutrients.
Branching filaments of actinomycetes bridge the dry gaps between soil particles, and their capsules and mucilaginous sheaths help them stick to surfaces.

Habitats and how bacteria cope

Habitat	How bacteria cope
Hot springs (up to 85^\circ\mathrm{C})	Thermophilic cyanobacteria and Aquificales
Freshwater, saltwater, damp places	Photosynthetic cyanobacteria and purple and green bacteria
Soil	Actinomycetes with filaments; saprotrophic bacteria that break down waste
Anaerobic swamps and sediments	Anaerobic and facultative bacteria; methanogens (archaea)
Human body	Normal flora, and parasitic bacteria with virulence factors

Metabolic diversity

Bacteria obtain carbon and energy in many ways: photosynthetic and chemoautotrophic bacteria make their own food, while saprotrophic and parasitic bacteria use organic matter. They can also be aerobic, anaerobic, facultative or microaerophilic, so they can live where oxygen is present or absent.

Rapid reproduction

Binary fission (Fig 6.9)

The DNA is replicated and the cell elongates.
The cell membrane invaginates and a cross wall forms, dividing the cell into two compartments.
Two genetically identical daughter cells are formed, each able to grow and divide.

Because one bacterium gives two cells, the population grows exponentially. One bacterium gives 16 bacteria after four generations, and under favourable conditions E. coli can double in about 20 minutes (p.162). This rapid growth lets bacteria colonize new habitats quickly.

38 marks

Differentiate between conjugation, transformation, and transduction in bacteria, elucidating their respective functions.

Solution

Comparison

Feature	Conjugation	Transformation	Transduction
Agent	Plasmid, transferred through a bridge between living cells	Free DNA released by dead or dividing bacteria	Bacteriophage (a virus that infects bacteria)
Contact between cells	Direct cell-to-cell contact	No contact; DNA is taken up from the medium	No contact; the phage carries the DNA
Material transferred	Mainly plasmid DNA, sometimes chromosomal genes	Fragments of DNA	Fragments of bacterial DNA packaged in the phage
Function	Genetic recombination: the recipient gets new genes	Recipient gains genes from the DNA it absorbs	Genetic exchange between bacteria by viruses

Mechanisms

Figures 6.10 and 6.11: conjugation passes a plasmid through a bridge, transduction carries a DNA fragment by a bacteriophage, and transformation takes up free DNA. The accent marks the transferred DNA.

Conjugation (Lederberg and Tatum, 1946)

The donor cell (with the plasmid) and the recipient cell make contact through a bridge-like connection.
The plasmid is replicated in the donor, and one copy passes through the bridge.
The recipient now carries the plasmid and its genes, so it is a recombinant cell.

Transduction

A bacteriophage injects its DNA into a bacterium.
The phage DNA may enter the host chromosome as a prophage, or it may make new phages.
When new phages are released, some carry fragments of bacterial DNA.
A phage carrying bacterial DNA infects another cell, and the fragment is built into its chromosome.

Transformation

Dying or rapidly dividing bacteria release fragments of their DNA into the surroundings.
A fragment is absorbed by a recipient cell of a species that can take up DNA.
The fragment joins the recipient chromosome, which becomes a transformed cell.

Function

All three processes move genes between bacteria. They are the sexual reproduction of bacteria because they produce recombinants with new combinations of genes, which increases variation and lets bacteria evolve by selection on their genetic material (p.164 to 165).

48 marks

Provide an overview of bacteria's morphology, dimensions, and structural characteristics.

Solution

Morphology

Bacteria have three main shapes:

Shape	Arrangement	Example
Spherical (cocci)	Pairs (diplococci), chains (streptococci), clumps (staphylococci), groups of four (tetrads), packets of eight (octads)	Streptococcus pneumoniae, Neisseria meningitidis
Rod-shaped (bacilli)	Pairs (diplobacilli), very short (coccobacilli), comma-shaped (vibrios), stacks (palisades)	Escherichia coli, Pseudomonas
Spiral	Thin-walled flexible rods usually single (spirochaetes)	Treponema pallidum

Dimensions

Bacteria range from about 0.1 to 600 \mum in one dimension, so they are much smaller than most eukaryotic cells.

Structure of a typical bacterial cell

Figure 6.1(b): A typical bacterial cell, with the cell wall, cytoplasmic membrane, mesosome, ribosomes, inclusions, chromosomal DNA (nucleoid), plasmid DNA, flagellum and pili.

Cell wall: the outermost layer, made of peptidoglycan; absent only in Mycoplasma species.
Cytoplasmic membrane: a phospholipid bilayer with infoldings called mesosomes.
Cytoplasm: contains many ribosomes and inclusions; there is no membrane-bound nucleus or organelle.
Genetic material: a single circular chromosome in the nucleoid, plus accessory plasmids.
Surface structures: a capsule (polysaccharide), flagella for motility and pili for adhesion. Endospores are formed by some species under stress.

58 marks

Elaborate on the significant economic contributions of bacteria.

Solution

Beneficial bacteria

Area	Contribution	Example
Digestion	Break down cellulose, starch and complex carbohydrates; emulsify fats	Bacteria in the intestines of cattle
Vitamins	Synthesis of vitamin K and vitamin B12	Escherichia coli
Industry	Acetic acid, acetone, lactic acid, butanol; cheese and tobacco flavourings; tanning of leather	Acetic acid bacteria, cheese strains
Food industry	Yogurt, cheese and butter	Specific bacterial strains
Medicine	Antibiotics such as streptomycin, auromycin and tetramycin	Mostly actinomycetes
Energy	Methane from sewage, dung and garbage (biogas)	Biogas plants in villages
Food protein	Single cell protein from cultivated microorganisms	Bacteria, yeast, fungi and algae
Biotechnology	Insulin, growth hormones, clotting factor VII, vaccines	Genetically engineered bacteria
Environment	Clean up oil spills (bioremediation); extraction of copper, uranium and gold	Oil-eating bacteria

Harmful bacteria

Acids produced by bacteria turn wine into vinegar.
Bacteria cause the decay of wood, leather and fabrics and spoil food by decomposition.
Parasitic bacteria cause diseases in plants (leaf spots, blights, soft rots, wilts and galls) and in man (cholera, typhoid, tuberculosis and pneumonia).

Overall, bacteria are more useful than harmful. Their benefits in food, medicine and industry far outweigh the damage they cause, and control measures are used against the harmful species (Section 6.9).

68 marks

Present a comprehensive account of Archaea, a distinct domain of microorganisms.

Solution

Introduction

Archaea (from the Greek archaios, ancient) were first called archaebacteria. They are prokaryotic cells that often live in extreme environments resembling the early Earth. Research has shown that they are distinct from bacteria, so they form their own domain.

Unifying features

They have special branched lipids in their membranes, which help them live in very hot or acidic places.
Their cell walls do not contain peptidoglycan.
Some archaea produce methane.
Many can make their own food using hydrogen, sulphur, carbon dioxide and water.
Their genetic and molecular features, such as ribosomal RNA, differ from those of bacteria.

Comparison with bacteria (Table 6.1)

Main feature	Eubacteria	Archaea
rRNA sequences	Many unique to eubacteria	Many match eukaryotes
RNA polymerase	Relatively small and simple	Complex, similar to eukaryotes
Introns	Absent	Present in some genes
Peptidoglycan in cell wall	Present	Absent
Membrane lipids	Carbon chains unbranched	Carbon chains branched

Groups of archaea

Group	Habitat	Example
Methanogens	Anaerobic settings: swamps, marshes and the intestines of humans and animals	Methanobacterium smithii (human gut)
Halophiles	Salty environments, such as heavily salted fish and meat	Halobacterium halobium
Thermoacidophiles	Hot and acidic conditions: hot springs, geysers and volcanic areas	Thermoplasma acidophilum, Thermus aquaticus

Phylogenetic position

In 1977 Carl Woese showed that archaea have a separate evolutionary lineage, which established the three-domain system. The most recent common ancestor of bacteria and archaea is believed to have been a hyperthermophile that lived 2.5 to 3.2 billion years ago.

Note. The book prints the halophile as 'Holobacterium halobium'; the genus is Halobacterium. The book also lists Thermus aquaticus as an archaean, but it is a bacterium. The book names the methanogen Methanobacterium smithii, a species now placed in the genus Methanobrevibacter.

76 marks

Explain the applications of bacteria in both research and technology.

Solution

Use in research

Microorganisms such as bacteria, yeast and Neurospora have been used extensively in research.
Lederberg and Tatum (1946) showed that bacteria exchange genes, and their experiment proved genetic recombination in E. coli.
In 1952 Hershey and Chase used the T2 bacteriophage and bacteria to prove that DNA is the hereditary material.

Use in technology

Application	How bacteria are used	Example
Biotechnology products	Transgenic bacteria clone a gene or mass-produce a product	Insulin, growth hormones, clotting factor VII, vaccines
Plant protection	Genetically engineered bacteria protect plants and reduce frost damage	Frost-plus bacteria changed to frost-minus
Bioremediation	Oil-eating bacteria are engineered to clean beaches after oil spills	Beaches after oil spills
Chemical production	Engineered bacteria synthesize organic chemicals	Phenylalanine
Mineral processing	Bacteria extract copper, uranium and gold from low-grade ores	Low-grade sources

88 marks

Investigate the remarkable diversity in bacterial nutrition strategies.

Solution

Bacteria are classified by how they obtain carbon and energy. Carbon metabolism is either autotrophic (carbon from carbon dioxide) or heterotrophic (carbon from organic compounds).

Classification of bacterial nutrition by carbon source and energy source, with examples from the book.

Autotrophic bacteria

Group	Energy and carbon	Examples
Photosynthetic	Light energy; \ce{H2S} replaces water as the hydrogen donor; no oxygen produced except in cyanobacteria	Green sulphur, purple sulphur and purple non-sulphur bacteria
Chemosynthetic	Oxidation of inorganic substances; carbon dioxide fixed into carbohydrate	Nitrifying bacteria and sulphur bacteria

\ce{2H2S + O2 -> 2S + H2O + Energy}

Heterotrophic bacteria

Group	How they feed	Examples
Saprotrophic	Secrete extracellular enzymes that break down dead plants, animals and debris, then absorb the products	Pseudomonas, Azobacter
Parasitic: obligate	Depend completely on the host to complete their life cycle	Rickettsia
Parasitic: facultative	Do not need a host and can live independently	Escherichia coli
Pathogenic parasites	Use toxins and virulence factors to enter tissues and take nutrients	Streptococcus pneumoniae, Salmonella typhi, Mycobacterium tuberculosis, Vibrio cholerae

Oxygen requirement (respiration)

Aerobic: need oxygen, such as Pseudomonas.
Anaerobic: cannot use oxygen, such as Spirochaeta.
Facultative: grow with or without oxygen, such as E. coli.
Microaerophilic: need only a low concentration of oxygen, such as Campylobacter.

Together, these strategies let bacteria use almost every source of carbon and energy on Earth, from sunlight and inorganic chemicals to the waste and tissues of other organisms.

96 marks

Contemplate how the absence of bacteria might have altered life on Earth.

Solution

The following is a reasoned answer built on the book's account of bacterial roles. Bacteria are unique in their ecological and biochemical functions, so their absence would have changed life in several ways.

Nutrient cycles would stop

Nitrogen fixation, nitrification and denitrification depend on bacteria (p.166). Without them, nitrogen gas would not be converted into ammonium that plants can use, and legumes could not grow with Rhizobium in their nodules.

Decomposition would fail

Bacteria and fungi are nature's decomposers. Without them dead plants and animals would not be broken down, humus would not form and nutrients would stay locked in dead matter.

Oxygen and the early atmosphere

Cyanobacteria are believed to have introduced oxygen into the primitive atmosphere (p.152). Without them the atmosphere might have stayed largely free of oxygen, so the aerobic life that now dominates Earth might never have developed.

Effects on animals and humans

Digestion of cellulose and starch in herbivores would be impossible without gut bacteria.
Vitamin K and B12 would not be synthesized in the gut.
The immune system would not develop normally, since normal flora helps shape it early in life (p.171).
Biotechnology, antibiotics, dairy products and biogas would not exist.

Conclusion

Bacteria would be missed most in the cycles that keep soil fertile and in the processes that recycle matter. Life might have remained simple, with fewer organisms able to grow in oxygen-rich, nutrient-rich conditions.

108 marks

Analyze the key roles played by prokaryotes in the biosphere and human society.

Solution

Roles in the biosphere

Producers: cyanobacteria and other photosynthetic bacteria fix carbon and release oxygen.
Recyclers: saprotrophic bacteria break down organic matter, release nutrients and carbon dioxide, and form humus (p.166).
Nitrogen cycle: bacteria carry out nitrogen fixation, ammonification, nitrification and denitrification (Figure below).
Symbionts: cyanobacteria live in partnership with liverworts, ferns and fungi (lichens), and coral.
Pathogens: parasitic bacteria cause diseases of plants and animals.

The nitrogen cycle with the bacteria that drive each step: fixation by Rhizobium, ammonification by saprotrophic bacteria, nitrification by Nitrosomonas and Nitrobacter, and denitrification by denitrifying bacteria.

Roles in human society

Area	Role of prokaryotes
Food	Yogurt, cheese and butter; vitamins in the gut; single cell protein
Medicine	Antibiotics from actinomycetes; normal flora protects and supports the body
Industry	Acetic acid, acetone, lactic acid and butanol
Energy and environment	Biogas from waste; bioremediation of oil spills
Technology and research	Insulin and other proteins; genetic recombination and DNA research
Health risk	Causes of cholera, typhoid, tuberculosis, pneumonia and plant diseases

Conclusion

Prokaryotes sustain the biosphere through photosynthesis, nutrient cycling and decomposition, and they serve human society through food, medicine and industry. Their harmful species, however, make hygiene and preventive measures essential.

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.

MCQ 62026 Annual I, Set B, MCQ 61 mark

Which vitamin is commonly produced by intestinal bacteria?

AVitamin A
BVitamin C
CVitamin KAnswer
DVitamin D

Why

The bacterial flora of the colon make vitamin K and B vitamins, which the body absorbs. Vitamins A, C and D are not made by gut bacteria: A and C come from the diet, and D is made in the skin in sunlight.

MCQ 142025 Annual I, Set B, MCQ 141 mark

The organism having Chlorophyll - a, Phycocyanin and Heterocyst may be a/an:

ABacterium
BCyanobacteriumAnswer
CFungus
DAlga

Why

Chlorophyll-a with the blue pigment phycocyanin (a phycobilin) and nitrogen-fixing heterocysts are the features of cyanobacteria. A plain bacterium (A) does not have these combined; fungi (C) are non-photosynthetic; algae (D) have chlorophyll but no phycocyanin-bearing heterocysts and are eukaryotes. Cyanobacteria are called blue-green algae but are bacteria.

Q.2 (ii) OR2025 Annual I, Set B, Q.2 (ii) OR1x3 = 3 marks

Enlist any three physical methods used to control bacteria with their mechanisms.

Solution

Moist heat (steam, boiling, pasteurisation): the heat causes coagulation of protein in the microbe, so it dies. Milk is pasteurised at 71^\circ\mathrm{C} for 15 seconds.
Dry heat (hot air): heat oxidises the parts of the microbe and kills it. Both dry and moist heat are used in microbiology laboratories.
Radiation: electromagnetic radiation below 300 nm, for example gamma rays, kills micro-organisms and is used for sterilisation. (A membrane filter removes bacteria from heat-sensitive liquids such as antibiotics and sera.)

Q.2 (iii) OR2025 Annual I, Set B, Q.2 (iii) OR3 marks

Endospore formation is a mechanism in bacteria to survive under unfavorable conditions. Justify.

Solution

Why the bacterium forms a spore (1 mark)

When nutrients run short or temperature and dryness become extreme, bacteria such as Bacillus and Clostridium undergo sporulation instead of dying: the cell forms one endospore inside itself.

How the spore resists (1 mark)

The core holds the DNA, a little cytoplasm and ribosomes, with very little water.
Several membranes, a peptidoglycan cortex and a thick keratin-like protein coat surround it.
So it withstands high temperature, drying, chemicals and lack of nutrients.

Structure of an endospore inside the mother cell: the layers protect the core.

Return to active life (1 mark)

The spore stays dormant until the mother cell ruptures and releases it. When conditions are favourable again it takes in water, germinates and grows into a vegetative cell. Since one cell makes one spore, this is survival, not reproduction.

Q.2 (v) OR2026 Annual I, Set B, Q.2 (v) OR1x3 = 3 marks

Compare photosynthetic bacteria and chemosynthetic bacteria. (Three points)

Solution

Point	Photosynthetic bacteria	Chemosynthetic bacteria
Source of energy	Sunlight (light energy)	Energy released by oxidising inorganic substances (for example sulphur compounds, ammonia)
Pigment	Contain bacteriochlorophyll, built into the membrane or scattered in the cytoplasm	Colourless; no light-trapping pigment
Hydrogen source and by-product	Use hydrogen sulphide (\ce{H2S}) instead of water, so sulphur is released	Energy comes from oxidising the inorganic compound; no light needed
Examples	Green sulphur, purple sulphur and purple non-sulphur bacteria	Nitrifying bacteria and sulphur bacteria

Both groups are autotrophic: they build carbohydrate from carbon dioxide. They differ only in the source of energy used to do it.

Note. Three points are asked; the table gives four, so write any three.

Q.2 (vi) OR2026 Annual I, Set B, Q.2 (vi) OR1x3 = 3 marks

Briefly explain three physical methods to control bacteria.

Solution

Moist heat (steam, boiling, pasteurisation): the heat causes coagulation of protein in the microbe, so it dies. Milk is pasteurised at 71^\circ\mathrm{C} for 15 seconds.
Dry heat (hot air): heat oxidises the parts of the microbe and kills it. Both dry and moist heat are used in microbiology laboratories.
Radiation: electromagnetic radiation below 300 nm, for example gamma rays, kills micro-organisms and is used for sterilisation. (A membrane filter removes bacteria from heat-sensitive liquids such as antibiotics and sera.)

Q.2 (viii) OR2026 Annual I, Set B, Q.2 (viii) OR1x3 = 3 marks

Enlist three advantages of endospore formation.

Solution

Survival of extreme conditions: the spore resists high temperature, drying (desiccation), and exposure to chemicals and most poisons, so the bacterium outlives shortage of water and nutrients.
Protection of the genetic material: the DNA, a little cytoplasm and ribosomes lie in the core, shielded by several membranes, a peptidoglycan cortex and a thick protein (keratin-like) coat.
Dormancy and recovery: the dehydrated spore stays dormant for a long time and, when conditions improve, germinates into an active vegetative cell that can grow and reproduce.

Q.2 (ix) OR2025 Annual I, Set B, Q.2 (ix) OR1x3 = 3 marks

Name and briefly explain Growth Phases of bacteria. (Any three)

Solution

Phase	What happens
Lag phase	Bacteria adapt to the new medium and may make new enzymes to digest its nutrients; growth has not yet reached its maximum rate.
Log (exponential) phase	Conditions are favourable; cells divide repeatedly and growth is at its maximum rate, a straight line when \log N is plotted against time.
Stationary phase	Nutrients are used up and toxic wastes build up, so the death rate equals the reproduction rate; the number of living cells stays constant.
Death (decline) phase	The death rate exceeds reproduction, cells stop multiplying and the number of living bacteria falls.

Growth curve of a bacterial population

Typical growth curve (\log_{10}N is the logarithm of the number of living bacteria): lag, log (exponential), stationary and death (decline) phases.

MCQ 62026 Annual I, Set D, MCQ 61 mark

Gut bacteria helps in the synthesis of:

AVitamin KAnswer
BProteins
CLipids
DDNA

Why

The bacterial flora of the gut make vitamin K (and B vitamins). Proteins, lipids and DNA are made by the body's own cells from the digested food; gut bacteria help digestion and vitamin supply but are not the source of these.

MCQ 72025 Annual I, Set D, MCQ 71 mark

Type of flagella arrangement shown in bacteria is:

ALophotrichous
BPeritrichousAnswer
CAmphitrichous
DMonotrichous

Why

The drawing shows flagella spread all over the surface of the cell. That is the peritrichous arrangement (peri = around). Lophotrichous has a tuft of flagella at a pole, amphitrichous has one flagellum at each end, and monotrichous has a single flagellum.

Arrangements of flagella in bacteria (the figure in the question is the last one).

MCQ 82025 Annual I, Set D, MCQ 81 mark

Genetic material moves from donor to recipient bacterium in:

ABinary fission
BConjugationAnswer
CTransduction
DTransformation

Why

In conjugation a plasmid (sometimes part of the chromosome) passes directly from a donor to a recipient cell through a bridge-like connection. Binary fission (A) only copies DNA into daughter cells and moves nothing between cells. Transduction (C) and transformation (D) also transfer DNA, but by a bacteriophage and by free DNA taken up from the surroundings; the question describes direct donor-to-recipient transfer, which is conjugation.

Note. Transduction and transformation also involve a donor and a recipient cell in the book, so the question relies on conjugation being the direct cell-to-cell transfer.

MCQ 172025 Annual I, Set D, MCQ 171 mark

The structures which help bacteria to survive under unfavorable conditions include:

AFlagella and pili
BPili and akinetes
CEndospores and plasmidAnswer
DFlagella and heterocyst

Why

Endospores are the survival structures of bacteria such as Bacillus and Clostridium. Of the pairs offered, C is the best match: it names endospores and plasmids (which carry extra genes). A is wrong because flagella and pili are for movement and attachment or gene transfer; B pairs pili (not a survival structure) with akinetes (resting cells of cyanobacteria); D pairs flagella with heterocysts, which fix nitrogen.

Note. Endospores are certainly right. The book does not say plasmids help survival, but B is excluded by pili and D by flagella and heterocyst, so C is the answer by elimination.

Q.2 (iv) OR2025 Annual I, Set D, Q.2 (iv) OR1x3 = 3 marks

Write any three chemical methods with their mechanisms used to control bacteria.

Solution

Disinfectants: kill or inhibit bacteria on surfaces and non-living objects in hospitals, laboratories and homes. Examples: bleach (sodium hypochlorite), hydrogen peroxide, quaternary ammonium compounds.
Antiseptics: chemicals used on living tissues such as skin and mucous membranes to prevent or treat infection. Examples: alcohol-based hand sanitisers, iodine-based antiseptics.
Preservatives: added to food and cosmetics to inhibit the growth of bacteria so that the product lasts longer. Examples: sodium benzoate, potassium sorbate, parabens. (Chlorine and chloramine disinfect drinking water; sulphonamides and nitrofurans are used in chemotherapy.)

Q.2 (vi) OR2026 Annual I, Set D, Q.2 (vi) OR1x3 = 3 marks

Briefly explain three chemical methods to control bacteria.

Solution

Disinfectants: kill or inhibit bacteria on surfaces and non-living objects in hospitals, laboratories and homes. Examples: bleach (sodium hypochlorite), hydrogen peroxide, quaternary ammonium compounds.
Antiseptics: chemicals used on living tissues such as skin and mucous membranes to prevent or treat infection. Examples: alcohol-based hand sanitisers, iodine-based antiseptics.
Preservatives: added to food and cosmetics to inhibit the growth of bacteria so that the product lasts longer. Examples: sodium benzoate, potassium sorbate, parabens. (Chlorine and chloramine disinfect drinking water; sulphonamides and nitrofurans are used in chemotherapy.)

Q.2 (viii)2026 Annual I, Set D, Q.2 (viii)3 marks

Enlist six stages of endospore formation.

Solution

Initiation: under unfavourable conditions (lack of nutrients, extreme temperature) sporulation begins and the DNA replicates, giving two identical copies.
Asymmetric division: the cell divides unequally into a larger mother cell and a smaller forespore.
Membrane development: several protective membranes form around the forespore.
Peptidoglycan layer: the mother cell lays down layers of peptidoglycan around the forespore (the cortex).
Spore coat formation: the mother cell makes a tough protein coat around the spore.
Maturation: the endospore dehydrates, so its water content falls greatly.

The book lists a seventh stage, release: the mother cell ruptures and frees the mature endospore, which stays dormant until conditions improve. Write this too if the question allows seven.

Note. The book gives seven stages; the question asks for six, so the first six are listed and release is added as a remark.

Q.2 (x) OR2025 Annual I, Set D, Q.2 (x) OR1x3 = 3 marks

How is photosynthesis in Cyanobacteria different from Bacteria? (any three differences)

Solution

Point	Cyanobacteria	Other photosynthetic bacteria (purple and green)
Pigments	Chlorophyll a, chlorophyll b and phycobiliproteins (phycocyanin, phycoerythrin)	Bacteriochlorophylls (purple bacteria) or chlorosomes with bacteriochlorophyll c (green sulphur bacteria)
Site	Thylakoids stacked as grana, as in chloroplasts	Pigments in the cell membrane, in infoldings called chromatophores; no thylakoids
Oxygen	Water is split and oxygen is released, as in plants	Most do not release oxygen; they use sulphur compounds or other molecules as electron donors
Light absorbed	A broad spectrum including blue and red	Mainly infrared and near-infrared

Exam focus

Compare the methods used to control bacteria: three physical methods (heat, radiation, filtration) with how each works. (short)
Asked as 3-mark OR parts in 2026 Set B Q.2 (vi) and 2025 Set B Q.2 (ii); book short question 9.
Go to answer
Name three chemical methods to control bacteria with their mechanism and an example each (disinfectants, antiseptics, preservatives). (short)
Asked in 2026 Set D Q.2 (vi) and 2025 Set D Q.2 (iv); book short question 8.
Go to answer
Endospore formation: stages, structure of the spore, advantages and why it is survival and not reproduction. (short)
Three papers asked it: 2026 Set B Q.2 (viii) OR (advantages), 2026 Set D Q.2 (viii) (six stages), 2025 Set B Q.2 (iii) OR (justify survival); book short question 16 and MCQ 10.
Go to answer
Photosynthesis in cyanobacteria compared with other photosynthetic bacteria (pigments, site, oxygen, light absorbed), and photosynthetic against chemosynthetic bacteria. (short)
2025 Set D Q.2 (x) and 2026 Set B Q.2 (v) OR asked these tables; 2025 Set B MCQ 14 tests the cyanobacteria pigments and heterocyst.
Go to answer
Phases of the bacterial growth curve: lag, log, stationary and death, with the curve drawn and labelled. (short)
2025 Set B Q.2 (ix) OR asked any three phases; the book gives a growth-curve skills activity.
Go to answer
Flagella arrangements (monotrichous, amphitrichous, lophotrichous, peritrichous) and identifying them from a drawing. (mcq)
2025 Set D MCQ 7 gave a drawing of a peritrichous cell; book exercise MCQ 7.
Go to answer
Gene transfer in bacteria: conjugation, transduction and transformation, and which one moves a plasmid from donor to recipient. (long)
2025 Set D MCQ 8 (conjugation); book long question 3 asks the full differentiation and MCQ 8 the plasmid.
Go to answer
Benefits of the normal bacterial flora, especially vitamin K and B vitamins made in the gut. (mcq)
Both 2026 sets asked in MCQ 6 which vitamin gut bacteria make (vitamin K); book short question 19.
Go to answer