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BCH 417 (Carbohydrate Biochemistry) Note

POLYSACCHARIDES

Polysaccharides are complex biomolecules or carbohydrate polymers consisting of more

than two monosaccharides linked together covalently by glycosidic linkages in a condensation

reaction. Commonly found monomer units in polysaccharides are glucose, fructose, mannose and

galactose which are simple sugars. Being comparatively large macromolecules, polysaccharides

are most often insoluble in water.

Polysaccharides are extremely important in organisms for the purposes of energy storage

and structural integrity.

Types of Polysaccharides

Polysaccharides can be broadly classified into two classes:

1. Homo-polysaccharides: These polysaccharides are made up of one type of

monosaccharide units. For example, cellulose, starch, glycogen.

2. Hetero-polysaccharides: These polysaccharides are made up of two or more types of

monosaccharide units. For example, hyaluronic acid and they provide extracellular

support for organisms.

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Structure of Polysaccharide

All polysaccharides are formed by the same basic process where monosaccharides are

connected via glycosidic bonds. These glycosidic bonds consist of an oxygen molecule bridging

two carbon rings. The bond is formed when a hydroxyl group is lost from the carbon of one

molecule, while the hydrogen is lost by the hydroxyl group of another monosaccharide. Because

two molecules of hydrogen and one of oxygen are expelled, the reaction is a dehydration

reaction. The structure of the molecules being combined determines the structures and properties

of the resulting polysaccharide.

A polysaccharide used for energy storage will give easy access to the constituent

monosaccharides whereas a polysaccharide used for support is usually a long chain of

monosaccharides that form fibrous structures.

Functions of Polysaccharides

Polysaccharides form a crucial part of cell function and structure. Nutrition

polysaccharides are common sources of energy, many organisms can easily break down starches

into glucose however, most organisms cannot metabolize cellulose or other polysaccharides like

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chitin and arabinoxylans. These carbohydrate types can be metabolized by some bacteria and

protists. Ruminants and termites, for example, use microorganisms to process cellulose. Even

though these complex polysaccharides are not very digestible, they provide important dietary

elements for humans, called dietary fiber, these carbohydrates enhance digestion among other

benefits. The main action of dietary fiber is to change the nature of the contents of the

gastrointestinal tract, and to change how other nutrients and chemicals are absorbed.

Soluble fiber binds to bile acids in the small intestine, making them less likely to enter

the body this in turn lowers cholesterol levels in the blood.

A. Storage Polysaccharides: Examples (Starch and Glrcogen);

Polysaccharides such as starch and glycogen are called storage polysaccharides because they

are stored in the liver and muscles to be converted to energy later for body functions. Starch is

found in plants whereas glycogen is found in animals.

1. Starch:

Starch is a glucose polymer in which glucopyranose units are bonded by alpha-linkages. It is

made up of a mixture of amylose (15–20%) and amylopectin (80–85%). Amylose consists of a

linear chain of several hundred glucose molecules, and Amylopectin is a branched molecule

made of several thousand glucose units (every chain of 24–30 glucose units is one unit of

Amylopectin).

Starches are insoluble in water and can be digested by breaking the alpha-linkages

(glycosidic bonds). Both humans and other animals have amylases, so they can digest

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starches. Food sources like; Potato, rice, wheat, and maize are major sources of starch in the

human diet. The formations of starches are the ways that plants store glucose.

2. Glycogen:

Glycogen serves as the secondary long-term energy storage in animals, with the primary

energy stores being held in adipose tissue. Glycogen is made primarily by the liver and the

muscles, but can also be made by glycogenesis within the brain and stomach.

Glycogen is analogous to starch, a glucose polymer in plants, and is sometimes referred to as

animal starch, having a similar structure to amylopectin but more extensively branched and

compact than starch. Glycogen is a polymer of α(1→4) glycosidic bonds linked, with α(1→6)-

linked branches. Glycogen is found in the form of granules in the cytosol/cytoplasm in many cell

types, and plays an important role in the glucose cycle.

Glycogen forms an energy reserve that can be quickly mobilized to meet a sudden need for

glucose, but one that is less compact and more immediately available as an energy reserve than

triglycerides (lipids).

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In the liver hepatocytes, glycogen can compose up to 8 percent (100–120 grams in an adult)

of the fresh weight soon after a meal. Only the glycogen stored in the liver can be made

accessible to other organs. In the muscles, glycogen is found in a low concentration of one to two

percent of the muscle mass. The amount of glycogen stored in the body, especially within the

muscles, liver, and red blood cells, varies with physical activity, basal metabolic rate, and eating

habits such as intermittent fasting.

Small amounts of glycogen are found in the kidneys, and even smaller amounts in certain

glial cells in the brain and white blood cells. The uterus also stores glycogen during pregnancy,

to nourish the embryo.

Glycogen is composed of a branched chain of glucose residues. It is stored in liver and

muscles. Glycogen is an energy reserve for animals, it is the chief form of carbohydrate stored in

animal body, it is insoluble in water, It turns brown-red when mixed with iodine, and it also

yields glucose on hydrolysis.

Structure of Glycogen

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B. Structural Polysaccharides: Examples (Arabinoxylans, Cellulose and Chitins

1. Arabinoxylans

These are found in both the primary and secondary cell walls of plants and are the

copolymers of two sugars: arabinose and xylose. They may also have beneficial effects on

human health.

2. Cellulose

The structural components of plants are formed primarily from cellulose. Wood is largely

cellulose and lignin, while paper and cotton are nearly pure cellulose. Cellulose is a polymer

made with repeated glucose units bonded together by beta-linkages.

Humans and many animals lack an enzyme to break the beta-linkages, so they do not digest

cellulose. Certain insects such as termites can digest cellulose, because bacteria possessing the

enzyme are present in their gut.

Cellulose is insoluble in water. It does not change color when mixed with iodine. On hydrolysis,

it yields glucose. It is the most abundant carbohydrate in nature.

3. Chitin

Chitin is one of many naturally occurring polymers. It forms a structural component of many

animals, such as exoskeletons. Over time it is bio-degradable in the natural environment. Its

breakdown may be catalyzed by enzymes called chitinases, secreted by microorganisms such as

bacteria and fungi, and produced by some plants. Some of these microorganisms have receptors

to simple sugars from the decomposition of chitin. If chitin is detected, they then produce

enzymes to digest it by cleaving the glycosidic bonds in order to convert it to simple sugars and

ammonia.

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Chemically, chitin is closely related to chitosan (a more water-soluble derivative of chitin). It

is also closely related to cellulose in that it is a long unbranched chain of glucose derivatives.

Both materials contribute structure and strength, protecting the organism

MUCOPOLYSACCHARIDES

Mucopolysaccharides are long chains of sugar molecules that are found throughout the

body, often in mucus and in fluid around the joints. They are more commonly called

glycosaminoglycans.

Glycosaminoglycans or mucopolysaccharides are long linear polysaccharides consisting

of repeating disaccharide units (i.e. two-sugar units). The repeating two-sugar unit consists of a

uronic sugar and an amino sugar, with the exception of keratan, where in the place of the uronic

sugar it has galactose. Because glycosaminoglycan are highly polar and attract water, they are

used in the body as a lubricant or shock absorber.

Production of Mucopolysaccharides

Glycosaminoglycans or mucopolysaccharides vary greatly in molecular mass,

disaccharide construction, and sulfation. This is because glycosaminoglycans synthesis is not

template driven like proteins or nucleic acids, but constantly altered by processing enzymes.

Glycosaminoglycans are classified into four groups based on core disaccharide structures;

1. Heparin/heparan sulfate (HSGAGs) and

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2. Chondroitin sulfate/dermatan sulfate (CSGAGs) are synthesized in the Golgi apparatus,

where protein cores made in the rough endoplasmic reticulum are post-translationally modified

with O-linked glycosylations by glycosyltransferases forming proteoglycans.

3. Keratan sulfate may modify core proteins through N-linked glycosylation or O-linked

glycosylation of the proteoglycan.

4. Hyaluronic acid is synthesized by integral membrane synthases which immediately

secrete the dynamically elongated disaccharide chain.

1. Hyaluronic Acid

Hyaluronic acid (HA) has the simplest structure of all mucopolysaccharides and does not

require additional sulfation of functional groups in the Golgi apparatus as do as the other

mucopolysaccharides. Instead, the structure consists of sequentially bound glucuronic acid and

N-acetylglucosamine residues. These monosaccharide building blocks are synthesized in the cell

cytoplasm and are recruited to the plasma membrane by diffusion for hyaluric acid synthesis.

After synthesis within the plasma membrane, hyaluric acid gets secreted from the cell into

the extracellular space unmodified.

2. Heparan Sulfate/Heparin

Heparan sulfate (HS) and heparin (Hep) contain repeating disaccharide units of N-

acetylglucosamine and hexuronic acid residues. The hexuronic acid residue glucuronic acid is

seen in heparan sulfate, while iduronic acid is present in heparin. Sulfation of the various

hydroxyl groups or the amino group present on the glucosamine compound of heparin

sulfate/heparin determines its ability to interact with various proteins, cytokines, and growth

factors, and ultimately its bioactive function. Heparin sulfate/heparin is tethered to A p-

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glycoprotein core via a serine residue connected to a tetrasaccharide linker consisting of one

xylose, two galactose, and one glucuronic acid residue.

3. Chondroitin Sulfate/Dermatan Sulfate

Chondroitin sulfate (CS) and dermatan sulfate (DS) are similar in structural composition to

heparin sulfate. Their disaccharide repeat consists of N-acetylgalactosamine and hexuronic acids,

iduronic acid in CS and glucuronic acid in dermatan sulfate. They are tethered to a P-

glycoprotein core via the same serine residue and tetrasaccharide linker as heparin sulfate.

Similar to heparin sulfate/heparin, the sulfation pattern of chondroitin sulfate/dermatan sulfate

that takes place in the Golgi apparatus determines the biological activity of the resulting

compound. Chondroitin sulfate polysaccharide chains linked to carrier proteins range in their

number of repeat units from 10 to 200 and are found both on cell surfaces and in the extracellular

matrix.

4. Keratan Sulfate

Keratan sulfate (KS) contains the disaccharide repeat consisting of galactose and N-

acetylglucosamine. Sulfation patterns may be present on either unit of the disaccharide repeat of

keratin sulfate with increased frequency on the N-acetylglucosamine residue. Keratan sulfate is

the only sulfated mucopolysaccharide that is not connected to the P-glycoprotein core by a

tetrasaccharide linker compound. Instead, the subtypes of keratin sulfate including KSI, KSII,

and KSIII each use a unique mechanism for P-glycoprotein core linkage. KS type I

glycosaminoglycan or mucopolysaccharide chains are tethered to a P-glycoprotein core by a

complex glycan structure utilizing an asparagine amino acid link. Keratan sulfate type II chains

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are predominantly found in cartilage and utilize an N-acetylgalactosamine link via a serine or

threonine residue. Kerartan sulfate type III are most frequency noted in brain tissue and use a

mannose linker to the protein core via serine or threonine residues.

Mucopolysaccharidoses

Mucopolysaccharidoses comprise a group of rare genetic diseases characterized by a

deficiency of lysosomal enzymes required for the metabolism of glycosaminoglycans. This

deficit results in lysosomal accumulation of glycosaminoglycans intermediates that eventually

leads to cellular dysfunction and death. Mucopolysaccharidoses manifest with variable

symptoms depending on the dysfunctional enzyme and associated expression of affected

glycosaminoglycans metabolism in organ systems.

Initial diagnostic steps of mucopolysaccharidoses following clinical suspicion include

urinary glycosaminoglycans and enzyme assays. Confirmatory testing for

mucopolysaccharidosis is via molecular diagnosis. Initially, treatment for

mucopolysaccharidoses had their basis around symptom management. However, both enzyme

replacement therapy and hematopoietic stem cell transplantation have been successfully used to

treat certain subgroups of mucopolysaccharidosis.

GLYCOPROTEINS

Glycoproteins are proteins which contain oligosaccharide chains (glycans) covalently

attached to amino acid side-chains. The carbohydrate is attached to the protein in a

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cotranslational or posttranslational modification. This process is known as glycosylation.

Secreted extracellular proteins are often glycosylated. Carbohydrates are attached to some

proteins to form glycoproteins.

In proteins that have segments extending extracellularly, the extracellular segments are

also often glycosylated. Glycoproteins are also often important integral membrane proteins,

where they play a role in cell–cell interactions. It is important to distinguish endoplasmic

reticulum-based glycosylation of the secretory system from reversible cytosolic-nuclear

glycosylation. Glycoproteins of the cytosol and nucleus can be modified through the reversible

addition of a single N-acetyl glucosamine residue that is considered reciprocal to

phosphorylation and the functions of these are likely to be additional regulatory mechanism that

controls phosphorylation-based signalling.

In contrast, classical secretory glycosylation can be structurally essential. For example,

inhibition of asparagine-linked, i.e. N-linked, glycosylation can prevent proper glycoprotein

folding and full inhibition can be toxic to an individual cell.

In contrast, perturbation of glycan processing (enzymatic removal/addition of

carbohydrate residues to the glycan), which occurs in both the endoplasmic reticulum and Golgi

apparatus, is dispensable for isolated cells (as evidence by survival with glycosides inhibitors)

but can lead to human disease (congenital disorders of glycosylation) and can be lethal in animal

models. It is therefore likely that the fine processing of glycans is important for endogenous

functionality, such as cell trafficking, but that this is likely to have been secondary to its role in

host-pathogen interactions. A famous example of this latter effect is the ABO blood group

system.

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Glycoproteins are always found on the outside of the plasma membrane, with the sugar

facing out. This is an image of the plasma membrane with glycoproteins labeled.

Diagram to show location of glycoproteins in the biological membrane

Functions of Glycolipids

Glycoproteins are involved in nearly every process in cells. They have diverse functions

such as in our immune system, protection of our body, communication between cells, and our

reproductive systems.

1. Immunology

White blood cells move along blood vessels, to look for potential invaders. The way they

attach to the blood vessel lining is through glycoproteins called lectins. Without these, our

immune system would be very weak, since our white blood cells would not be able to travel the

body.

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Glycoproteins are also important for red blood cells. Blood type refers to the type of

glycoprotein on our red blood cells. If you have type A blood, you have A antigens, or A

glycoproteins, on your red blood cells. This helps the body to identify that your blood is part of

you and tells it not to attack it. Glycoproteins also help to stimulate the process of coagulation of

platelets to clot blood when there is a cut. People who are missing important proteins on platelets

can't clot their blood and have a disease called hemophilia, where any cut continues to bleed

indefinitely.

2. Protection

Many organs in the body need to secrete mucus to function properly. Examples include the

stomach, small intestine, and airways in the lungs. Cells lining these body cavities secrete, or

send out, glycoproteins. The sugars mixed with water in the body create a smooth mucus. In the

stomach, this mucus helps protect the stomach lining from the harsh acids needed to digest food.

In the lungs, the mucus helps to trap bacteria, keeping the lungs clean and healthy.

Glyoproteins are also involved in keeping the skin healthy. Glycoproteins are on the surface

of skin cells, called epithelial cells. These help to attach the skin cells to each other, forming a

tough barrier to protect our body. Cadherins are an example of a glycoprotein that helps our

skin hold together. In the image seen here, the long black lines connecting two skin cells together

are types of cadherins. Think of them like glue holding our skin together.

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STRUCTURE AND SYNTHESIS OF BACTERIA CELL WALL

The bacterium contains a well-developed cell structure which is responsible for some of its

unique biological structures and pathogenicity. Many structural features are unique to bacteria

and are not found among archaea or eukaryotes. Because of the simplicity of bacteria relative to

larger organisms and the ease with which they can be manipulated experimentally, the cell

structure of bacteria has been well studied, revealing many biochemical principles that have been

subsequently applied to other organisms.

Bacterial cells lack a membrane bound nucleus. Their genetic material is naked within the

cytoplasm. Ribosomes are their only type of organelle.

The term “nucleoid” refers to the region of the cytoplasm where chromosomal DNA is

located, usually a singular, circular chromosome. Bacteria are usually single-celled, except when

they exist in colonies. These ancestral cells reproduce by means of binary fission, duplicating

their genetic material and then essentially splitting to form two daughter cells identical to the

parent. A wall located outside the cell membrane provides the cell support, and protection

against mechanical stress or damage from osmotic rupture and lysis.

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Diagram of a Bacteria Cell Wall

The major component of the bacterial cell wall is peptidoglycan or murein. This rigid

structure of peptidoglycan, specific only to prokaryotes, gives the cell shape and surrounds the

cytoplasmic membrane. Peptidoglycan is a huge polymer of disaccharides (glycan) cross-linked

by short chains of identical amino acids (peptides) monomers. The backbone of the

peptidoglycan molecule is composed of two derivatives of glucose: N-acetylglucosamine (NAG)

and N-acetlymuramic acid (NAM) with a pentapeptide coming off N-acetylmuramic acid and

varying slightly among bacteria. The N-acetylglucosamine and N-acetylmuramic strands are

synthesized in the cytosol of the bacteria. They are connected by inter-peptide bridges. They are

transported across the cytoplasmic membrane by a carrier molecule called bactoprenol. From

the peptidoglycan inwards all bacterial cells are very similar. Going further out, the bacterial

world divides into two major classes: Gram positive (Gram +) and Gram negative (Gram -). The

cell wall provides important ligands for adherence and receptor sites for viruses or antibiotics.

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The gram-positive cell wall

Gram-positive cell walls are thick and the peptidoglycan (also known as murein) layer

constitutes almost 95% of the cell wall in some gram-positive bacteria and as little as 5-10% of

the cell wall in gram-negative bacteria. The gram-positive bacteria take up the crystal violet dye

and are stained purple. The cell wall of some gram-positive bacteria can be completely dissolved

by lysozymes which attacks the bonds between N-acetylmuramic acid and N-acetylglucosamine.

In other gram-positive bacteria, such as Staphylococcus aureus, the walls are resistant to

the action of lysozymes. They have O-acetyl groups on carbon-6 of some muramic acid residues.

The matrix substances in the walls of gram-positive bacteria may be polysaccharides or

teichoic acids. The latter are very widespread, but have been found only in gram-positive

bacteria. There are two main types of teichoic acid ribitol teichoic acids and glycerol teichoic

acids. The latter one is more widespread. These acids are polymers of ribitol phosphate and

glycerol phosphate, respectively, and only located on the surface of many gram-positive bacteria.

However, the exact function of teichoic acid is debated and not fully understood. A major

component of the gram-positive cell wall is lipoteichoic acid. One of its purposes is providing an

antigenic function. The lipid element is to be found in the membrane where its adhesive

properties assist in its anchoring to the membrane.

The gram-negative cell wall

Gram-negative cell walls are much thinner than the gram-positive cell walls, and they

contain a second plasma membrane superficial to their thin peptidoglycan layer, in turn adjacent

to the cytoplasmic membrane. Gram-negative bacteria are stained as pink colour. The chemical

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structure of the outer membrane's lipopolysaccharide is often unique to specific bacterial sub-

species and is responsible for many of the antigenic properties of these strains.

PLASMA MEMBRANE

The plasma membrane or bacterial cytoplasmic membrane is composed of a phospholipid

bilayer and thus has all of the general functions of a cell membrane such as acting as a

permeability barrier for most molecules and serving as the location for the transport of molecules

into the cell. In addition to these functions, prokaryotic membranes also function in energy

conservation as the location about which a proton motive force is generated. Unlike eukaryotes,

bacterial membranes (with some exceptions e.g. Mycoplasma and methanotrophs) generally do

not contain sterols. However, many microbes do contain structurally related compounds called

hopanoids which likely fulfill the same function. Unlike eukaryotes, bacteria can have a wide

variety of fatty acids within their membranes. Along with typical saturated and unsaturated fatty

acids, bacteria can contain fatty acids with additional methyl, hydroxy or even cyclic groups. The

relative proportions of these fatty acids can be modulated by the bacterium to maintain the

optimum fluidity of the membrane (e.g. following temperature change).

Gram-negative and mycobacteria have an inner and outer bacteria membrane. As a

phospholipid bilayer, the lipid portion of the bacterial outer membrane is impermeable to

charged molecules. However, channels called porins are present in the outer membrane that

allow for passive transport of many ions, sugars and amino acids across the outer membrane.

These molecules are therefore present in the periplasm, the region between the cytoplasmic and

outer membranes. The periplasm contains the peptidoglycan layer and many proteins responsible

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for substrate binding or hydrolysis and reception of extracellular signals. The periplasm is

thought to exist in a gel-like state rather than a liquid due to the high concentration of proteins

and peptidoglycan found within it. Because of its location between the cytoplasmic and outer

membranes, signals received and substrates bound are available to be transported across the

cytoplasmic membrane using transport and signaling proteins imbedded there.

EXTRA-CELLULAR STRUCTURES OF BACTERIA

1. Fimbriae and pili

Fimbriae (sometimes called attachment pili) are protein tubes that extend out from the outer

membrane in many members of the Proteobacteria. They are generally short in length and

present in high numbers about the entire bacterial cell surface. Fimbriae usually function to

facilitate the attachment of a bacterium to a surface (e.g. to form a biofilm) or to other cells (e.g.

animal cells during pathogenesis). A few organisms (e.g. Myxococcus) use fimbriae for motility

to facilitate the assembly of multicellular structures such as fruiting bodies.

Pili are similar in structure to fimbriae but are much longer and present on the bacterial cell

in low numbers. Pili are involved in the process of bacterial conjugation where they are called

conjugation pili or sex pili. Type IV pili (non-sex pili) also aid bacteria in gripping surfaces.

2. S-layers

An S-layer (surface layer) is a cell surface protein layer found in many different bacteria and

in some archaea, where it serves as the cell wall. All S-layers are made up of a two-dimensional

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array of proteins and have a crystalline appearance, the symmetry of which differs between

species. The exact function of S-layers is unknown, but it has been suggested that they act as a

partial permeability barrier for large substrates. For example, an S-layer could conceivably keep

extracellular proteins near the cell membrane by preventing their diffusion away from the cell. In

some pathogenic species, an S-layer may help to facilitate survival within the host by conferring

protection against host defence mechanisms.

3. Glycocalyx

Many bacteria secrete extracellular polymers outside of their cell walls called glycocalyx.

These polymers are usually composed of polysaccharides and sometimes protein. Capsules are

relatively impermeable structures that cannot be stained with dyes such as India ink. They are

structures that help protect bacteria from phagocytosis and desiccation. Slime layer is involved in

attachment of bacteria to other cells or inanimate surfaces to form biofilms. Slime layers can also

be used as a food reserve for the cell.

4. Flagella

This is perhaps the most recognizable extracellular bacterial cell structure. The flagella are

whip-like structures protruding from the bacterial cell wall and are responsible for bacterial

motility (i.e. movement). The arrangement of flagella about the bacterial cell is unique to the

species observed. Common forms include:

I. Monotrichous ; Single flagellum

II. Lophotrichous ; A tuft of flagella found at one of the cell poles

III. Amphitrichous; Single flagellum found at each of two opposite poles

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IV. Peritrichou; Multiple flagella found at several locations about the cell

The bacterial flagellum consists of three basic components: a whip-like filament, a motor

complex, and a hook that connects them. The filament is approximately 20 nm in diameter and

consists of several protofilaments, each made up of thousands of flagellin subunits. The bundle is

held together by a cap and may or may not be encapsulated. The motor complex consists of a

series of rings anchoring the flagellum in the inner and outer membranes, followed by a proton-

driven motor that drives rotational movement in the filament.

INTRA-CELLULAR STRUCTURE

In comparison to eukaryotes, the intracellular features of the bacterial cell are extremely

simple. Bacteria do not contain organelles in the same sense as eukaryotes. Instead, the

chromosome and ribosomes are the only easily observable intracellular structures found in all

bacteria. There do exist, however, specialized groups of bacteria that contain more complex

intracellular structures, some of which are the following

1. The bacterial DNA and plasmids

Unlike eukaryotes, the bacterial DNA is not enclosed inside of a membrane-bound nucleus

but instead resides inside the bacterial cytoplasm. This means that the transfer of cellular

information through the processes of translation, transcription and DNA replication all occur

within the same compartment and can interact with other cytoplasmic structures, most notably

ribosomes. Bacterial DNA can be located in two places:

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a. Bacterial chromosome, located in the irregularly shaped region known as the nucleoid

b. Extrachromosomal DNA, located outside of the nucleoid region as circular or linear

plasmids

The bacterial DNA is not packaged using histones to form chromatin as in eukaryotes but

instead exists as a highly compact supercoiled structure, the precise nature of which remains

unclear. Most bacterial chromosomes are circular although some examples of linear DNA exist

(e.g. Borrelia burgdorferi). Usually a single bacterial chromosome is present, although some

species with multiple chromosomes have been described. Along with chromosomal DNA, most

bacteria also contain small independent pieces of DNA called plasmids that often encode for

traits that are advantageous but not essential to their bacterial host. Plasmids can be easily gained

or lost by a bacterium and can be transferred between bacteria as a form of horizontal gene

transfer. So plasmids can be described as an extra chromosomal DNA in a bacterial cell.

2. Ribosomes and other multiprotein complexes

In most bacteria the most numerous intracellular structure is the ribosome, the site of protein

synthesis in all living organisms. All prokaryotes have 70S (where S=Svedberg units) ribosomes

while eukaryotes contain larger 80S ribosomes in their cytosol. The 70S ribosome is made up of

a 50S and 30S subunits. The 50S subunit contains the 23S and 5S rRNA while the 30S subunit

contains the 16S rRNA. These rRNA molecules differ in size in eukaryotes and are complexed

with a large number of ribosomal proteins, the number and type of which can vary slightly

between organisms. While the ribosome is the most commonly observed intracellular

multiprotein complex in bacteria other large complexes do occur and can sometimes be seen

using microscopy.

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3. Intracellular membranes

Not very typical of all bacteria, some microbes contain intracellular membranes in addition to

(or as extensions of) their cytoplasmic membranes. An early idea was that bacteria might contain

membrane folds termed mesosomes, but these were later shown to be artifacts produced by the

chemicals used to prepare the cells for electron microscopy. Examples of bacteria containing

intracellular membranes are phototrophs, nitrifying bacteria and methane-oxidising bacteria.

Intracellular membranes are also found in bacteria belonging to the poorly studied

Planctomycetes group, although these membranes more closely resemble organellar membranes

in eukaryotes and are currently of unknown function. Chromatophores are intracellular

membranes found in phototrophic bacteria. Used primarily for photosynthesis, they contain

bacteriochlorophyll pigments and carotenoids.

4. Cytoskeleton

The prokaryotic cytoskeleton is the collective name for all structural filaments in

prokaryotes. It was once thought that prokaryotic cells did not possess cytoskeletons, but recent

advances in visualization technology and structure determination have shown that filaments

indeed exist in these cells. In fact, homologues for all major cytoskeletal proteins in eukaryotes

have been found in prokaryotes. Cytoskeletal elements play essential roles in cell division,

protection, shape determination, and polarity determination in various prokaryotes.

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5. Nutrient storage structures

Most bacteria do not live in environments that contain large amounts of nutrients at all times.

To accommodate these transient levels of nutrients bacteria contain several different methods of

nutrient storage in times of plenty for use in times of want. For example, many bacteria store

excess carbon in the form of polyhydroxyalkanoates or glycogen. Some microbes store soluble

nutrients such as nitrate in vacuoles. Sulfur is most often stored as elemental (S0) granules which

can be deposited either intra or extra-cellularly. Sulfur granules are especially common in

bacteria that use hydrogen sulfide as an electron source. Most of the above-mentioned examples

can be viewed using a microscope and are surrounded by a thin non-unit membrane to separate

them from the cytoplasm.

6. Inclusions

Inclusions are considered to be nonliving components of the cell that do not possess

metabolic activity and are not bounded by membranes. The most common inclusions are

glycogen, lipid droplets, crystals, and pigments. Volutin granules are cytoplasmic inclusions of

complexed inorganic polyphosphate. These granules are called metachromatic granules due to

their displaying the metachromatic effect; they appear red or blue when stained with the blue

dyes methylene blue or toluidine blue.

7. Gas vacuoles

Gas vacuoles are membrane-bound, spindle-shaped vesicles, found in some planktonic

bacteria and Cyanobacteria, that provides buoyancy to these cells by decreasing their overall cell

density. Positive buoyancy is needed to keep the cells in the upper reaches of the water column,

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so that they can continue to perform photosynthesis. They are made up of a shell of protein that

has a highly hydrophobic inner surface, making it impermeable to water (and stopping water

vapour from condensing inside) but permeable to most gases. Because the gas vesicle is a hollow

cylinder, it is liable to collapse when the surrounding pressure increases. Natural selection has

fine tuned the structure of the gas vesicle to maximise its resistance to buckling, including an

external strengthening protein, GvpC, rather like the green thread in a braided hosepipe. There is

a simple relationship between the diameter of the gas vesicle and pressure at which it will

collapse – the wider the gas vesicle the weaker it becomes. However, wider gas vesicles are more

efficient, providing more buoyancy per unit of protein than narrow gas vesicles. Different

species produce gas vesicle of different diameter, allowing them to colonise different depths of

the water column (fast growing, highly competitive species with wide gas vesicles in the top

most layers; slow growing, dark-adapted, species with strong narrow gas vesicles in the deeper

layers). The diameter of the gas vesicle will also help determine which species survive in

different bodies of water. Deep lakes that experience winter mixing expose the cells to the

hydrostatic pressure generated by the full water column. This will select for species with

narrower, stronger gas vesicles.

The cell achieves its height in the water column by synthesising gas vesicles. As the cell rises

up, it is able to increase its carbohydrate load through increased photosynthesis. Too high and the

cell will suffer photobleaching and possible death, however, the carbohydrate produced during

photosynthesis increases the cell's density, causing it to sink. The daily cycle of carbohydrate

build-up from photosynthesis and carbohydrate catabolism during dark hours is enough to fine-

tune the cell's position in the water column, bring it up toward the surface when its carbohydrate

levels are low and it needs to photosynthesis, and allowing it to sink away from the harmful UV

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radiation when the cell's carbohydrate levels have been replenished. An extreme excess of

carbohydrate causes a significant change in the internal pressure of the cell, which causes the gas

vesicles to buckle and collapse and the cell to sink out.

8. Microcompartments

Bacterial microcompartments are widespread, membrane-bound organelles that are made of a

protein shell that surrounds and encloses various enzymes that provide a further level of

organization; they are compartments within bacteria that are surrounded by polyhedral protein

shells, rather than by lipid membranes. These "polyhedral organelles" localize and

compartmentalize bacterial metabolism, a function performed by the membrane-bound

organelles in eukaryotes.

9. Carboxysomes

Carboxysomes are bacterial microcompartments found in many autotrophic bacteria such as

Cyanobacteria, Knallgasbacteria, Nitroso- and Nitrobacteria. They are proteinaceous structures

resembling phage heads in their morphology and contain the enzymes of carbon dioxide fixation

in these organisms (especially ribulose bisphosphate carboxylase/oxygenase, RuBisCO, and

carbonic anhydrase). It is thought that the high local concentration of the enzymes along with the

fast conversion of bicarbonate to carbon dioxide by carbonic anhydrase allows faster and more

efficient carbon dioxide fixation than possible inside the cytoplasm. Similar structures are known

to harbor the coenzyme B12-containing glycerol dehydratase, the key enzyme of glycerol

fermentation to 1,3-propanediol, in some Enterobacteriaceae (e. g. Salmonella).

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10. Magnetosomes

Magnetosomes are bacterial microcompartments found in magnetotactic bacteria that allow

them to sense and align themselves along a magnetic field (magnetotaxis). The ecological role of

magnetotaxis is unknown but is thought to be involved in the determination of optimal oxygen

concentrations. Magnetosomes are composed of the mineral magnetite or greigite and are

surrounded by a lipid bilayer membrane. The morphology of magnetosomes is species-specific.

ENDOSPORES

This is Perhaps the best known bacterial adaptation to stress. Endospores are bacterial

survival structures that are highly resistant to many different types of chemical and

environmental stresses and therefore enable the survival of bacteria in environments that would

be lethal for these cells in their normal vegetative form. Endospore formation is limited to

several genera of gram-positive bacteria such as Bacillus and Clostridium. It differs from

reproductive spores in that only one spore is formed per cell resulting in no net gain in cell

number upon endospore germination. The location of an endospore within a cell is species-

specific and can be used to determine the identity of a bacterium. Dipicolinic acid is a chemical

compound which composes 5% to 15% of the dry weight of bacterial spores and is implicated in

being responsible for the heat resistance of endospores.

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LIPOPROTEIN

Lipoproteins are special particles made up of droplets of fats surrounded by a single layer of phospholipid molecules. Phospholipids are molecules of fats which are attached to a phosphorus-containing group. They are distinctive in being amphipathic, which means they have both polar and non-polar ends.

In a lipoprotein, the polar ends of all the phospholipid molecules face outwards, so as to interact with water, itself a polar molecule. This enables the lipoprotein to be carried in the blood rather than rising to the top, like cream on milk. The non-polar fat balled up inside the phospholipid layer, at the center of the lipoprotein, is thus transported to the place where it must be stored or metabolized, through the bloodstream, despite being insoluble in blood. Thus lipoproteins are molecular level trucks to carry fats wherever they are required or stored.

Diagram showing Lipoproteins

Types of Lipoproteins

Different lipoproteins are differentiated based on specific proteins attached to the

phospholipid outer layer, called the apolipoprotein. This also helps to make the fatty molecule

more stable, and also binds to cell surface receptors in some cases, to enable the cell to take up

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the lipoprotein by receptor-mediated endocytosis. The types of lipoproteins with their function

are as follows:

1. Chylomicrons – these are the largest and least dense of the lipoproteins, with the highest

triglyceride content. They consist of a protein component synthesized in the liver, which

wraps around diet-derived cholesterol and fats. It travels from the intestinal lymphatics to

the large veins, and sticks to the inner surface of the tiny capillary blood vessels inside

the muscles and the fat storage cells in various parts of the body. There the fat is digested,

while the cholesterol remains. This is now called the chylomicron remnant. It travels to

the liver, where the cholesterol is metabolized. Thus chylomicrons deliver fats and

cholesterol from the intestines to the muscles, fat cells and the liver.

2. VLDL, very low density lipoprotein – this is composed of protein, fats and cholesterol

synthesized in the liver. It is associated with 5 different apoproteins, namely , B-100, C-I,

C-II, C-III and E. It is converted to IDL and LDL by removal of the apoproteins, except

for one called apoprotein B100, along with esterification of the cholesterol. They are

second only to chylomicrons in the percentage triglyceride content.

3. IDL – intermediate density lipoprotein, is created by the metabolism of VLDL.

4. LDL, low density lipoprotein – this is the last VLDL remnant, and contains chiefly

cholesterol. The only apoprotein associated with it is apoB-100. Thus all these forms

carry fats and cholesterol produced in the liver to the tissues.

5. HDL, high density lipoprotein – this has the highest protein: lipid ratio, and so is the

densest. It has the apoprotein A-1. This is also called ‘good cholesterol’, because it

carries cholesterol away from the tissues to the liver, lowering blood cholesterol levels.

High HDL levels are associated with lowered risk of cardiovascular disease. HDL levels

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are higher with exercise, higher estrogen levels, with alcohol consumption, and weight

loss.

Importance of Lipoprotein

Lipoproteins show varying patterns that correlate with the risk of having a fatal

cardiovascular event. High LDL, VLDL and triglyceride levels are associated with a high risk of

atherosclerosis and heart disease. High HDL is correlated with reduced cholesterol levels, and a

lower cardiovascular risk. Thus a high measurement of apo-A-1 correlates with a low

atherosclerosis risk. HDL levels drop with cigarette smoking, and rise with regular exercise,

alcohol use, estrogen levels and weight loss.

Lipid Profile

An important part of the health evaluation is the lipid profile. This consists of measuring

the total plasma cholesterol, the LDL, VLDL and HDL levels, as well as the triglyceride level.

These numbers are studied together with other risk factors in your history, to decide

whether treatment is required to bring down the cholesterol levels. High cholesterol does not

produce any signs or symptoms, so a blood test is essential to evaluate the risk of atherosclerosis.

All children should have one lipid profile between 9-11 years, and repeat it between 17-21 years.

Adults without other risk factors should have a blood lipid profile once in 5 years at least.

Effect of Lipid Profile on Diet

A diet high in saturated fat is associated with a high cholesterol level. However, if it

contains plenty of fish oils, which are rich in omega-3 unsaturated fats, the cholesterol and

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triglyceride levels drop dramatically. Monounsaturated and polyunsaturated fatty acids, as in

olive oil and peanut or sunflower oils, respectively, also reduce the blood cholesterol.

GLYCOLIPIDS

Glycolipids are lipids with a carbohydrate attached by a glycosidic (covalent) bond. Their

role is to maintain the stability of the cell membrane and to facilitate cellular recognition, which

is crucial to the immune response and in the connections that allow cells to connect to one

another to form tissues. Glycolipids are found on the surface of all eukaryotic cell membranes,

where they extend from the phospholipid bilayer into the extracellular environment.

Structure of Glycolipids

The essential feature of a glycolipid is the presence of a monosaccharide or

oligosaccharide bound to a lipid moiety. The most common lipids in cellular membranes are

glycerolipids and sphingolipids, which have glycerol or a sphingosine backbones, respectively.

Fatty acids are connected to this backbone, so that the lipid as a whole has a polar head and a

non-polar tail. The lipid bilayer of the cell membrane consists of two layers of lipids, with the

inner and outer surfaces of the membrane made up of the polar head groups, and the inner part of

the membrane made up of the non-polar fatty acid tails.

The saccharides that are attached to the polar head groups on the outside of the cell are

the ligand components of glycolipids, and are likewise polar, allowing them to be soluble in the

aqueous environment surrounding the cell. The lipid and the saccharide form a glycoconjugate

through a glycosidic bond, which is a covalent bond. The anomeric carbon of the sugar binds to a

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free hydroxyl group on the lipid backbone. The structure of these saccharides varies depending

on the structure of the molecules to which they bind.

Types of Glycolipids

1. Glycoglycerolipids:

This is a sub-group of glycolipids characterized by an acetylated or non-acetylated glycerol with

at least one fatty acid as the lipid complex. Glyceroglycolipids are often associated with

photosynthetic membranes and their functions. The subcategories of glyceroglycolipids depend

on the carbohydrate attached.

I. Galactolipids: this is defined by a galactose sugar attached to a glycerol lipid

molecule. They are found in chloroplast membranes and are associated with

photosynthetic properties.

II. Sulfolipids: this have a sulfur-containing functional group in the sugar moiety

attached to a lipid. An important group is the sulfoquinovosyl diacylglycerols

which are associated with the sulfur cycle in plants.

2. Glycosphingolipids:

This is a sub-group of glycolipids based on sphingolipids. Glycosphingolipids are mostly located

in nervous tissue and are responsible for cell signaling.

3. Cerebrosides:

This is a group glycosphingolipids involved in nerve cell membranes.

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I. Galactocerebrosides: this is a type of cerebroseide with galactose as the

saccharide moiety

II. Glucocerebrosides: this is a type of cerebroside with glucose as the

saccharide moiety; often found in non-neural tissue.

III. Sulfatides: this is a class of glycolipids containing a sulfate group in the

carbohydrate with a ceramide lipid backbone. They are involved in

numerous biological functions ranging from immune response to nervous

system signaling.

4. Gangliosides: this is the most complex animal glycolipids. They contain negatively

charged oligosacchrides with one or more sialic acid residues; more than 200 different

gangliosides have been identified. They are most abundant in nerve cells.

I. Globosides: glycosphingolipids with more than one sugar as part of the

carbohydrate complex. They have a variety of functions; failure to degrade these

molecules leads to Fabry disease.

II. Glycophosphosphingolipids: complex glycophospholipids from fungi, yeasts, and

plants, where they were originally called "phytoglycolipids". They may be as

complicated a set of compounds as the negatively charged gangliosides in

animals.

III. Glycophosphatidylinositols: a sub-group of glycolipids defined by a

phosphatidylinositol lipid moiety bound to a carbohydrate complex. They can be

bound to the C-terminus of a protein and have various functions associated with

the different proteins they can be bound to.

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Function of Glycolipids

1. Cell–cell interactions:

The main function of glycolipids in the body is to serve as recognition sites for cell–cell

interactions. The saccharide of the glycolipid will bind to a specific complementary carbohydrate

or to a lectin (carbohydrate-binding protein), of a neighboring cell. The interaction of these cell

surface markers is the basis of cell recognitions, and initiates cellular responses that contribute to

activities such as regulation, growth, and apoptosis.

2. Immune responses:

This is an example of how glycolipids function within the body is the interaction between

leukocytes and endothelial cells during inflammation. Selectins, a class of lectins found on the

surface of leukocytes and endothelial cells bind to the carbohydrates attached to glycolipids to

initiate the immune response. This binding causes leukocytes to leave circulation and congregate

near the site of inflammation. This is the initial binding mechanism, which is followed by the

expression of integrins which form stronger bonds and allow leukocytes to migrate toward the

site of inflammation. Glycolipids are also responsible for other responses, notably the

recognition of host cells by viruses.

3. Blood types

Blood types are an example of how glycolipids on cell membranes mediate cell interactions

with the surrounding environment. The four main human blood types (A, B, AB, O) are

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determined by the oligosaccharide attached to a specific glycolipid on the surface of red blood

cells, which acts as an antigen. The unmodified antigen, called the H antigen, is the characteristic

of type O, and is present on red blood cells of all blood types. Blood type A has an N-

acetylgalactosamine added as the main determining structure, type B has a galactose, and type

AB has all three of these antigens. Antigens which are not present in an individual's blood will

cause antibodies to be produced, which will bind to the foreign glycolipids. For this reason,

people with blood type AB can receive transfusions from all blood types (the universal acceptor),

and people with blood type O can act as donors to all blood types (the universal donor).

Metabolism of Glycolipids

1. Glycosyltransferases

Enzymes called glycosyltransferases link the saccharide to the lipid molecule, and also

play a role in assembling the correct oligosaccharide so that the right receptor can be activated on

the cell which responds to the presence of the glycolipid on the surface of the cell. The glycolipid

is assembled in the Golgi apparatus and embedded in the surface of a vesicle which is then

transported to the cell membrane. The vesicle merges with the cell membrane so that the

glycolipid can be presented on the cell's outside surface.

2. Glycoside hydrolases

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Glycoside hydrolases catalyze the breakage of glycosidic bonds. They are used to modify

the oligosaccharide structure of the glycan after it has been added onto the lipid. They can also

remove glycans from glycolipids to turn them back into unmodified lipids.

3. Defects in metabolism

Sphingolipidoses are a group of diseases that are associated with the accumulation of

sphingolipids which have not been degraded correctly, normally due to a defect in a glycoside

hydrolase enzyme. Sphingolipidoses are typically inherited, and their effects depend on which

enzyme is affected, and the degree of impairment. One notable example is Niemann–Pick

disease which can cause pain and damage to neural networks, and is usually fatal in early

infancy.