GLYCOLYSIS

In Glycolysis, Glucose; a six carbon molecule is degraded through sequential

enzyme dependent reactions into two molecules of pyruvic acid, a three carbon
compound.

Glucose is a stable molecule i.e. It has little tendency to breakdown into simpler
products. If the energy locked in its molecular configuration is to be released, the
glucose must first be made more reactive. A small amount of energy must be
invested by the cell to initiate glycolysis. It is adenosine tri phosphate (ATP) that
provides the energy for initiating glycolysis.

The first step in glycolysis is the transfer of phosphate group from ATP to No. 6
carbon of glucose. Adenosine di phosphate and glucose 6-phosphate are formed.

After an enzyme catalyses, the conversion of glucose 6-phosphate to its isomer

fructose-6-phosphate (F-6-P).

Another molecule of ATP is invested which transfers its phosphate group this time
to No. 1 carbon of F-6-P forming fructose- 1, 6-di phosphate and ADP. These
reactions are known as phosphorylation reactions because phosphate groups are
added to glucose and fructose molecules.

The next step in glycolysis is enzymatic splitting of fructose 1, 6-di phosphate into
two fragments. Each of these two molecules contains three carbon atoms. One is
called phosphoglycer aldehyde (PGAL) and other is Dihydroxy acetone phosphate
(DHAP). These two sugar molecules are isomers to each other and are
interconvertible. This is the reaction from which glycolysis derives its name.
Normally both these molecules are converted into pyruvic acid through subsequent
enzyme controlled reactions. Since two molecules of ATP are used this part of
glycolysis is the energy investment phase.

In the remaining part of glycolysis ATP molecules are synthesized hence it is

called energy yielding phase.

In the following reaction, an enzyme dehydrogenase and a co-enzyme

nicotinamide dinucleonde NAD + work together.

The enzyme strips off two hydrogen atoms from PGAL. These electrons are
captured by NAD + . This is a redox reaction where PGAL is oxidized by removal
of electrons and NAD is reduced by the addition of electrons.

With the loss of two hydrogen atoms PGAL is converted into phosphoglyceric acid
(PGA). Now PGA picks up phosphate group (Pi) present in cytoplasm and
becomes 1-3 di phosphoglyceric acid (DPGA).

In the very next step DPGA loses its phosphate group to ADP forming ATP and 3-
phosphoglyceric acid.
The phosphate group attached with carbon atom No. 3 of PGA changes its position
to carbon atom No. 2 forming an isomer 2- phosphoglyceric acid.

With removal of water molecule 2 PGA is converted into phospho-enol pyruvic

acid (PEPA).

Finally phosphate group is transferred to ADP forming ATP and pyruvic acid.

Synthesis of ATP during glycolysis is known as substrate level phosphorylation

because phosphate group is transferred directly to ADP from another molecule.

Glycolysis is the universal energy harvesting process of life. Metabolic

machinery of glycolysis is found in all organisms from unicellular bacteria and
yeasts to multicellular bodies of plants, animals and human beings. Glycolysis
occurs freely in anaerobic environment within cytoplasm without being associated
with organelle or membrane structure.

Net input and output of glycolysis can be summarized as under:

Looking back over glycolysis for energy yield, 4 ATP molecules are produced at
substrate level phosphorylation and 2 ATP molecules are consumed to initiate the
process. Thus there is net gain of two ATP molecules. The process also yields two
pairs of energized electrons and two NADH.
 What is Kreb's cycle?
 The Kreb's cycle is a stage of cellular respiration following glycolysis and used by all
aerobic organisms to release stored energy through the oxidation of acetyl-CoA. It
takes place in the mitochondria, consuming oxygen, producing carbon dioxide and
water as waste products, and converting ADP to energy-rich ATP.
Formation of Acetyl CoA
 Aerobes utilize molecular oxygen to extract large amount of energy from two products
of glycolysis i.e. Pyruvic acid and NADH+H. Pyruvic acid diffuses from cytoplasmic
fluid into mitochondrion, the site of Kreb’s cycle.
 Before entering into Kreb’s cycle it undergoes chemical changes. It loses one
molecule of CO2. The remaining 2 carbon fragments is oxidized to form acetyl
group. Finally Coenzyme A, a Sulphur containing compound derived from vitamin
B is attached to acetyl group.The product is Acetyl Coenzyme A.
 Acetyl CoA links glycolysis with Kreb’s cycle.
 Acetyl coenzyme A, a two carbon compound formed from pyruvic acid participates
cyclic series of reactions during which oxidation process is completed. This series of
cyclic reactions is called Kreb’s cycle or citric acid cycle.
Step 1: Acetyl CoA+ Oxaloacetate to Citrate.
 Enzyme: Citrate synthase.
 Reaction: Condensation.

Step 2: Citrate to cis- Aconitate.

 Enzyme: Aconitase.
 Reaction: Dehydration.

Step 3: Hydration of cis-Aconitate to isocitrate.

Step 4: Isocitrate to Alpha-Ketoglutarate.

 Enzyme: Isocitrate dehydrogenase.

 Reaction: Oxidative decarboxylation.

Dehydrogenation of isocitrate occurs and yields oxalosuccinate as an intermediate.

Then CO2 leaves to have alpha-Ketoglutarate. This reaction gives NADH.
 Step 5: Alpha-ketoglutarate to Succinyl CoA.

 Enzyme: Alpha-Ketoglutarate dehydrogenase complex.

 Reaction: Oxidative decarboxylation.
A Co2 molecule is lost and the remaining four carbon compound is oxidized by
transfer of a pair of electron reducing NAD to NADH. Then four carbon fragment
combines with CoA by an unstable bond forming Succinyl CoA.
 Step 6: Succinyl CoA to Succinate.
 Enzyme: Succinyl CoA synthetase.
 Reaction: Substrate level phosphorylation.
 CoA is replaced by phosphate group which is then transferred to Guanosine
diphosphate to form Guanosine tri phosphate. GTP transfers its phosphate group to
ADP forming ATP. With addition of water molecule succinic acid is formed.
 Step 7: Succinate to Fumarate.
 Enzyme: Succinate dehydrogenase.
 Reaction: Oxidation.
 Two hydrogens of succinate leave to an acceptor, FAD. Then this reaction yields
fumarate and FADH2.
 Step 8: Fumarate is converted into malate.
 Enzyme: Fumarase.
 Reaction: Hydration.
 With addition of H2O fumaric acid is converted into malic acid.
 Step 9: Malate to Oxaloacetate.
 Enzyme: Malate dehydrogenase.
 Reaction: Oxidation.
Malate is dehydrogenated to form oxaloacetate. The hydrogen acceptor is NAD. So
this reaction yields NADH
FERMENTATION
It is a derived from the Latin word fervere which mean to boil .it is the process
which living cell are able to obtain energy through the breakdown of glucose and
other simple. Fermentation is a metabolic process that consumes sugar in the absence
of oxygen. The products are organic acids, gases, or alcohol. It occurs in yeast and
bacteria, and also in oxygen-starved muscle cells, as in the case of lactic acid
fermentation. The science of fermentation is known as zymology.

In the 1920s it was discovered that, in the absence of air, extracts of muscle catalyze
the formation of lactate from glucose and that the same
intermediate compounds formed in the fermentation of grain are produced by
muscle. An important generalization thus emerged: that fermentation reactions are
not peculiar to the action of yeast but also occur in many other instances of glucose
utilization.

Types of fermentation

Alcoholic fermentation :This is also known as ethanol fermentation, is the

anaerobic pathway carried out by yeasts in which simple sugars are converted to
ethanol and carbon dioxide. The process of alcohol fermentation allows yeasts to
break down sugar in the absence of oxygen and results in byproducts that humans
benefit from.

Lactic acid fermentation: This is the process by which our muscle cells deal with
pyruvate during anaerobic respiration. When our cells need energy, they break
down simple molecules like glucose. The process for breaking down glucose
anaerobically is called glycolysis. Example : When in an anaerobic environment,
some cells can use glycolysis and fermentationto keep producing ATP. Lactic acid
fermentation happens in our muscle cells when we are exercising feverishly, while
alcoholic fermentation is used in yeast cells and is what leads to beer, bread, and
wine.
 LACTIC ACID FERMENTATION

WHAT IS LACTIC ACID?

• Lactic acid is an organic compound with the molecular formula C3H6O3 it was
first discovered in 1780 by Swedish chemist Carl Wilhelm Scheele who isolated
it from stale milk.
• Lactic acid relation to milk gives it its name lact- being the Latin word for milk.
• Its discovery in muscles occurred later in the year 1808 by Jacob Berzelius.
• Lactic acid is produced through a process known as lactic fermentation.
• Lactic fermentation occurs in many organisms but only during a specific
process known as anaerobic respiration.
• Muscles usually receives energy through a process known as cellular respiration
but when there is a lack of oxygen in the organism muscles go through
anaerobic respiration. Hence the glucose is converted into lactic acid.
• WHAT IS LACTIC ACID FERMENTATION?
• Lactic acid fermentation is a metabolic process by which glucose and other six
carbon sugars are converted into cellular energy in anaerobic condition.
• HOW DOES IT OCCURS?
• Lactic acid fermentation is a minor process which occurs after glycolysis in
anaerobic respiration.
• In this an enzyme found in every organism called lactate dehydrogenase
catalyze the reaction between NADH produced from glycolysis with the
pyruvate molecules to create the NAD necessary to begin glycolysis.
• Lactate is then formed as a byproduct of this reaction. The lactate is protonate
into lactic acid.
• This lactic acid continues building up in the muscles until oxygen is
reintroduced into the system and aerobic respiration begin.
• Once anaerobic exercise ends the lactic acid is sent to the liver and converted
back into pyruvate.
TYPES OF LACTIC ACID FERMENTATION
• There are two types of lactic acid fermentation homolactic or heterolactic
• In homolactic NADH reduces pyruvate directly to from lactate this process
does not release gas.
• In heterolactic lactate is further metabolized resulting in ethanol and CO2.
 • Lactic acid fermentation is performed by certain bacteria and fungi however
this type of fermentation also occurs in muscles cells in the absence of
oxygen.

PROKARYOTES

Cell theory : A view of scientist about cell is called cell theory. This was given by
Schieleden , Schwann and Rudolf Virchow. It states that :

1. All organisms are composed of one or more of cells.

2. Cell is the basic unit of life.

3. The new cell arises only from pre-existing cell

TYPES OF CELL

1. PROKARYOTIC CELL : The cell which has no well organized nucleus and no
membrane bounded organelles is called Prokaryotic cell such as bacteria and
cynobacteria

2. EUKARYOTIC CELL: The cell which has well organized nucleus and well
membrane bounded organelles such as plants and animals cell

DIFFERENCE BETWEEN PROKARYOTIC AND EUKARYOTIC CELL

 A major difference between prokaryotic and eukaryotic cells is the location of

chromosomes.
 In an eukaryotic cell, chromosomes are contained in a true nucleus
 In a prokaryotic cell, the DNA is concentrated in the nucleoid) without a
membrane separating it from the rest of the cell.
 In prokaryotic cell, DNA is a single strand or double strand DNA. But in
eukaryotic cell, DNA is double strand.
 The smallest bacteria, mycoplasmas, are between 0.1 to 1.0 micron.
 Most bacteria are 1-10 microns in diameter.
 Eukaryotic cells are typically 10-100 microns in diameter.
 STRUCTURE OF BACTERIA

Following structures are found in bacteria

Nucleoid : The nucleoid (meaning nucleus-like) is an irregularly shaped region

within the cell of a prokaryote that contains all or most of the genetic material,
called genophore. In contrast to the nucleus of a eukaryotic cell, it is not
surrounded by a nuclear membrane.

Genophore : Sometimes referred to as the bacterial chromosome, is a long

double strand of DNA, usually in one large circle. It includes most of the genetic
material of the organism.

Plasmid: Plasmids are small circular DNA fragments found in the cytoplasm that
contain code responsible for antibiotic resistance and other characteristics.
Plasmids and the associated traits can be transferred between bacteria, even from
one bacterial species to another.

Cytoplasm: This internal "soup" of the bacterial cell is bounded on the outside by
the cell envelope. The cytoplasm is mostly water, but within it are the bacterial
inclusions - nucleoid, plasmids, ribosomes and storage granules - as well as the
components necessary for bacterial metabolism.

Endospore: Some bacteria can survive hostile environments, often for long time
periods, by bundling their genetic material in a tough internal structure.
Endospores can withstand heat, cold, radiation, and lack of nutrition.

Ribosomes: Ribosomes give the cytoplasm of bacteria a granular appearance in

electron micrographs. Though smaller than the ribosomes in eukaryotic cells, these
inclusions have a similar function in translating the genetic message in messenger
RNA into the production of peptide sequences (proteins).

Cell Envelope

Beginning from the innermost structure and moving outward, bacteria have some
or all of the following structures:

Plasma Membrane: This is a lipid bilayer much like the cytoplasmic (plasma)
membrane of other cells. There are numerous proteins moving within or upon this
layer that are primarily responsible for transport of ions, nutrients and waste across
the membrane.

Periplasmic Space: This cellular compartment is found only in those bacteria that
have both an outer membrane and plasma membrane (e.g. Gram negative bacteria).
In the space are enzymes and other proteins that help digest and move nutrients
into the cell.

Cell Wall: Composed of peptidoglycan (polysaccharides + protein), the cell wall

maintains the overall shape of a bacterial cell. The three primary shapes in bacteria
are coccus (spherical), bacillus (rod-shaped) and spirillum (spiral). Mycoplasma
are bacteria that have no cell wall and therefore have no definite shape.

Outer Membrane: This lipid bilayer is found in Gram negative bacteria and is the
location of lipopolysaccharide (LPS) in these bacteria. Gram positive bacteria lack
this layer. LPS can be toxic to a host and can stimulate the host's immune system.

Capsule: This layer of polysaccharide (sometimes proteins) protects the bacterial

cell and is often associated with pathogenic bacteria because it serves as a barrier
against phagocytosis by white blood cells. Capsules can be seen by viewing
bacteria in India ink.

Appendages : Bacteria may have the following appendages.

Pili, Fimbriae: These hollow, hairlike structures made of protein allow bacteria to
attach to other cells. A specialized pilus, the sex pilus, allows the transfer of plasmid
DNA from one bacterial cell to another. Pili (sing., pilus) are also called fimbriae
(sing., fimbria).

Flagella: The purpose of flagella (sing., flagellum) is motility. Flagella are long
appendages which rotate by means of a "motor" in the cell envelope. Bacteria may
have one, a few, or many flagella in different positions on the cell.
 Nutritional requirements of microorganisms
◦ Nutrients: are substances used in biosynthesis and energy production. To obtain
energy and construct new cellular components, organisms must have a supply
of raw materials or nutrients. Microbial cell composition shows that 95% of cell
dry weight is made up of a few major elements: Carbon, oxygen, hydrogen,
nitrogen, sulfur, phosphorus, potassium, calcium, magnesium and iron.
Requirements for Carbon, hydrogen and oxygen:
◦ Carbon is needed for the skeleton or backbone of all organic molecules and
molecules serving as carbon sources normally also contribute both oxygen and
hydrogen atoms.
◦ The hub element for constructing cell material is carbon, so important that this
element is used to create another pair of categories for characterizing organisms
according to their nutritional needs.
◦ Autotrophs: use inorganic carbon in the form of carbon dioxide as their sole
source of carbon.
◦ Heterotrophs: require a supply of carbon in the form of organic molecules.
◦ Phototrophs: derive energy from sunlight through photosynthesis.
◦ Chemotrophs: depend on chemical energy harvested by the breaking of
chemical bonds. Chemical energy sources may be organic and inorganic
compounds.
◦ Organotrophs: organisms that use organic compounds, such as sugars and
amino acids for energy.
◦ Lithotrophs: Organisms that obtain energy from inorganic compounds
,especially those containing nitrogen, iron or sulfur.

◦ Requirements for nitrogen, phosphorus and sulfur:

◦ Nitrogen is needed for the synthesis of amino acids, purines, pyrimidines, some
carbohydrates and lipids, enzyme cofactors and other substances. Phosphorus is
needed for nucleic acids, phospholipids, ATP, several cofactors, some proteins
and other cell components. E.coli can use both organic and inorganic
phosphate. Sulfur is needed for synthesis of amino acids cysteine and
methionine, some carbohydrates biotin and thiamine.

◦ Organic growth factors: Many microorganisms have the enzymes and pathways
necessary to synthesize all cell components. Many lack one or more enzymes
 and hence require organic compounds because they are essential cell
components or precursors of such components and cannot be synthesized by the
organisms are called growth factors. There are three major classes of growth
factors:
◦ Amino acids: needed for protein synthesis.
◦ Purines and Pyrimidines: for nucleic acid synthesis.

◦ Vitamins: small organic molecules that usually make up all or part of enzyme
cofactors, and only very small amounts sustain growth.
◦ Certain microorganisms are capable of synthesizing their own required
vitamins, others must obtain them from their nutrient medium.
◦ Vitamin compounds that have been shown effective in microbial nutrition
include thiamine chloride, riboflavin, nicotinic acid, pantothenic acid,
pyridoxine, biotin, para-amino benzoic acid, folic acid, cyanocobalamin, and
inositol.

LIPID METABOLOISM
 These are polar organic compound generally insoluble in water and soluble in
non polar solvent like, Chloroform , Benzene , Ether , Acetone . It contains
carboxyl groups –cooH.

Types of lipid

Following are groups of lipids.

Fatty acids [saturated and unsaturated].

Glycerides [glycerol] containing lipids. Non glyceride lipid[ waxes, steroids]

Complex lipid [lipoproteins, glycolipids.

Phospholipid Cholesterols

Lipid digestion : Digestion is the first step of lipid metabolism and it is the process of
breaking the triglycerides down into small mono glyceride units with the help of
lipase enzyme. Digestion of fat begin in mouth through chemical digestion by lingual
lipase. Majority of the lipid digestion and absorption take place in intestines. Bile salt
are secreted into the small intestines to help breakdown the triglycerides.

Lipid absorption : The second step of lipid metabolism is the absorption of fat.
Absorption of fats occur only in small intestine .Once the triglycerides are broken
down into individual fatty acid and glycerol along with cholesterol, they will
aggregate into structures called micelles.

Role of lipid metabolism : Metabolism and function of fat in fish. Lipids and their fat
constituent fatty acid along with protein. Major organic constituent of fish they play
major role as the source of metabolic energy for the growth of body movement and
reproduction .

Lipid metabolism disorders : Lipid metabolism disorder are illnesses where trouble
occurs in breaking down or synthesizing fats or fat like substances. Lipid metabolism
disorder are associated with an increase in the concentration of plasma lipid. In the
blood such as LDL cholesterol VLDL and triglycerides which most commonly lead
cardiovascular disorder. Some of the heredity disorder occur due to parents

PROTEIN METABOLISM

AMINO ACID : Amino acids are molecules containing both amine and carboxyl
functional groups. In the alpha amino acids, the amino and carboxylate groups are
attached to the same carbon atom, which is called the α–carbon. The various alpha
amino acids differ in which side chain (R group) is attached to their alpha carbon.

AMINO ACID SYNTHESIS : Amino acid synthesis is the set of biochemical

processes (metabolic pathways) by which the various amino acids are produced
from other compounds. Amino acids are critical to life, and have a variety of roles
in metabolism. The substrates for these processes are various compounds in the
organism's diet or growth media. Not all organisms are able to synthesise all
amino acids, for example humans are only able to synthesise 12 of the 20 standard
amino acids.

PROTEIN : Proteins are essential nutrients for animal body. They are building
blocks of body tissues . Protein is needed by the animals for growth and
maintenance. Protein can found in all cells of the body, major structural component
of all cells. Present in organ, hair and skin.

Metabolism : Protein metabolism denotes the various biochemical processes

responsible for the synthesis of proteins and amino acids(anabolism), and the
breakdown of proteins and other large molecules, (catabolism) . Digestion breaks
protein down to amino acids. If amino acids are in excess of the body's biological
requirements, they are metabolized to glycogen or fat and subsequently used for
energy metabolism.If amino acids are to be used for energy their carbon skeletons
are converted to acetyl CoA, which enters the Krebs cycle for oxidation, producing
ATP. The final products of protein catabolism include carbon dioxide, water, ATP,
urea, and ammonia.

Protein Digestion : Protein breakdown begins in the stomach. No protein

hydrolyzing enzymes are found in saliva. Hydrolysis (10% of peptide bonds) &
denaturization by pepsin enzyme & HCl acid. Produce short chain polypeptides
in the stomach.Trypsin, chymotrypsin, & carboxypeptidase from Pancreatic
juices, and Amino peptidase from cells in the small intestine Brush Zone create
“free” amino acids . Free amino acids are absorbed through intestinal wall via
active transport. There are 3 sources of “free” amino acids:

1. Dietary protein breakdown

2. Biosynthesis of amino acids in the Liver
3. Protein turnover (I prefer apple turnovers) Protein turnover is the
breakdown & re-synthesis of body proteins.

In organic Nutrient requirement of microbes

• Nutrition: a process by which chemical substances (nutrients) are acquired

from the environment and used in cellular activities. Nutrient are very
essential substance used by microorganisims to Survive , growth and
reproduce. Nutrients are categorize according to Carbon content :

• Inorganic nutrients: A combination of atoms other than C and H

• Organic nutrients: Contain C and H, usually the products of living things

 Inorganic nutrients

Inorganic nutrients– atoms, ions or molecules that contains a combination of atoms

other than carbon and hydrogen.

 water

 phosphorus

 Potassium

 Sodium

 Calcium

 Magnesium

 Iron

 Zinc

 Copper

 Manganese, etc.

PHOSPHORUS:

 Main inorganic source of phosphorus is phosphate (PO43-)

1. Derived from phosphoric acid
2. Found in rocks and oceanic mineral deposits

 Key component of all nucleotides

 Phospholipids in cell membranes

 Coenzymes

Sulphur

 Widely distributed throughout the environment in mineral form

 Essential component of some vitamins

 Calcium

 Sources: Mineral deposits and oceans

 Calcium- stabilizer of cell walls and endospores.

Potasium

 Sources: Mineral deposits and oceans

• Potassium- protein synthesis and membrane function

SODIUM

• Sources : Mineral deposits and oceans

• Sodium- certain types of cell transport

magensium

• Sources: Mineral deposits and geological sediment

• Magnesium- component of chlorophyll and stabilizer of membranes and

ribosomes

IRON

• Sources : Mineral deposits and geological sediment

• Iron- important component of cytochrome proteins

ZINC

• Sources : various geological sediment

• Zinc- essential regulatory element for eukaryotic genetics, and binding

factors for enzymes

• Copper, cobalt, nickel, molybdenum, manganese, silicon, iodine, and boron-

needed in small amounts by some microbes but not others