LESSON 1: NUCLEIC ACIDS and Guanine pairs with Cytosine.

This pairing is
Nucleic acids  - molecules that allow organisms to known as the complementary base pairing
transfer genetic information from one generation to the because the DNA strands are complementary to
next. each other.
Stores the genetic information that determines traits Types of DNA
and makes protein synthesis possible. The helical structure of DNA is thus variable and
Include DNA and RNA. These molecules are composed depends on the sequence as well as the environment.
of long strands of nucleotides. 1. B-DNA - is the Watson–Crick form of the
Nucleic acids can be found within double helix.
the nucleus and cytoplasm of our cells. 2. A-DNA – Unlike B-DNA, the placement of base-
Nucleotides - composed of a nitrogenous base, a pair within the duplex are displaced away from
five-carbon sugar, and a phosphate group. the central axis and closer to the major groove.
Nucleic acids are composed The result is a ribbon-like helix with a more
of nucleotide monomers linked together. open cylindrical core in A-form.
Nucleotides have three parts: 3. Z-DNA - discovered by Rich, Nordheim &Wang
 A Nitrogenous Base - Include purine in 1984. It has antiparallel strands as B-DNA
molecules (adenine and guanine) and but is long and thin as compared to B-DNA. It
pyrimidine molecules (cytosine, thymine, and has a radically different duplex structure, with
uracil). the two strands coiling in left-handed helices
 A Five-Carbon (Pentose) Sugar - In DNA, and a pronounced zig-zag (hence the name)
the five-carbon sugar is deoxyribose, while pattern in the phosphodiester backbone.
ribose is the pentose sugar in RNA. Properties of DNA
 A Phosphate Group  . DNA exists as a pair of molecules rather than
. Phosphodiester linkages - form the sugar- a single molecule. These strands are entwined
phosphate backbone of both DNA and RNA. in the shape of a double helix and the helix is
Nucleotides are linked together by Phosphodiester kept stable by hydrogen bonds, which can be
bond to form polynucleotide chains found between the bases attached to the two
Two Examples of Nucleic Acids strands.
DNA (Deoxyribonucleic Acid) - is a long chain  Base pairing - is a defining property of DNA
molecule that plays a central role in life on earth. and was particularly exciting when it was first
The information encoded in strands of DNA controls the discovered because it suggested the 'copying'
genetic makeup of organisms. mechanism for DNA.
The function of DNA is to store all of the genetic  DNA Supercoiling - is a central property of
information that an organism needs to develop, DNA. DNA can be in a relaxed or coiled state
function, and reproduce. Essentially, it is the biological and it is this coiling that allows our extremely
instruction manual found in each of your cells. long strands of DNA to fit or 'pack' into the
It is found in the nucleus of eukaryotes and in the comparatively much smaller cells in our bodies.
chloroplasts and mitochondria. In prokaryotes, the DNA This supercoiling property makes DNA more
is not enclosed in a membranous envelope, but rather efficient by allowing it to make better use of
free-floating within the cytoplasm. space and fit neatly into a significantly smaller
space relative to its relaxed, longer size.
DNA Structure  DNA Conformations
DNA is made up of three components: RNA (Ribonucleic Acid) - is a polymer of nucleotides
1. a nitrogenous base which is made up of a ribose sugar, a phosphate, and
2. a pentose (five-carbon) sugar bases such as adenine, guanine, cytosine, and uracil.
3. a phosphate group - It is a polymeric molecule essential in various
biological roles in coding, decoding, regulation,
and expression of genes.
DNA - has a double-helix structure, with
- RNA is a nucleic acid messenger between DNA
sugar and phosphate on the outside of the helix,
and ribosomes, it serves as the genetic material
forming the sugar-phosphate backbone of the DNA.
in some organisms (viruses).
 The nitrogenous bases are stacked in the interior in
pairs, like the steps of a staircase; the pairs are
bound to each other by hydrogen bonds.
 The two strands of the helix run in opposite
directions. This antiparallel orientation is important
to DNA replication and in many nucleic acid
interactions. RNA STRUCTURE
 Base Pairs Only certain types of base pairing are - a single-stranded helix.
allowed. This means Adenine pairs with Thymine, - RNA is a long polymer consisting of nucleotides.
 - The strand has a 5′end (with a phosphate group) Transfer RNA (tRNA) - is the smallest of the 3 types
and a 3′end (with a hydroxyl group). of RNA having about 75-95 nucleotides.
- The ribonucleotides are linked together by 3′ –> are an essential component of translation, where their
5′ phosphodiester bonds. main function is the transfer of amino acids
- The nitrogenous bases that compose the during protein synthesis.
ribonucleotides include adenine, cytosine, tRNAs also act as adapters in the translation of the
uracil, and guanine, thus, the difference in the genetic sequence of mRNA into proteins. Therefore
structure of RNA from that of DNA include: they are also called adapter molecules.
- The bases in RNA are adenine (abbreviated A), Structure of tRNA
guanine (G), uracil (U) and cytosine (C). tRNAs have a clover leaf structure which is
- The sugar in RNA is ribose rather than stabilized by strong hydrogen bonds between the
deoxyribose as in DNA. nucleotides.
RNA Secondary Structure Anticodon - is a three-base nucleotide
Ribosomal RNAs (rRNAs) and transfer RNAs sequence that binds to the mRNA codon.
(tRNAs) exhibit substantial secondary structure, This interaction between codon and anticodon specifies
as do some messenger RNAs (mRNAs). the next amino acid to be added during protein
Types of RNA synthesis.
Function: Transfer RNA brings or transfers amino
acids to the ribosome that correspond to each three-
nucleotide codon of rRNA.
Properties of RNA
 RNA forms in the nucleolus, and then moves to
specialized regions of the cytoplasm depending
In both prokaryotes and eukaryotes, there are three on the type of RNA formed.
main types of RNA –  RNA, containing a ribose sugar, is more
Messenger RNA (mRNA) - Accounts for about 5% of reactive than DNA and is not stable in alkaline
the total RNA in the cell. conditions. RNA’s larger helical grooves mean
- Most heterogeneous of the 3 types of RNA in it is more easily subject to attack by enzymes.
terms of both base sequence and size, it  RNA strands are continually made, broken
carries the genetic code copied from the DNA down and reused.
during transcription in the form of triplets of  RNA is more resistant to damage from UV light
nucleotides called codons. than DNA.
- As part of post-transcriptional processing in  RNA’s mutation rate is relatively higher.
eukaryotes, the 5’ end of mRNA is capped Unusual bases may be present..
with a guanosine triphosphate nucleotide,  RNA is more versatile than DNA, capable of
which helps in mRNA recognition during performing numerous, diverse tasks in an
translation or protein synthesis. organism.
Function: mRNA transcribes the genetic code from
DNA into a form that can be read and used to make DNA REPLICATION
proteins. mRNA carries genetic information from the DNA replication - is the production of
nucleus to the cytoplasm of a cell. identical DNA helices from a single double-stranded
Ribosomal RNA (rRNA) - Found in the ribosomes and DNA molecule.
account for 80% of the total RNA present in the cell. - Each molecule consists of a strand from the
Ribosomes consist of two major components: original molecule and a newly formed strand.
 Small ribosomal subunits - which read the RNA, 1. Initiation - where the DNA uncoils and strands
 Large subunits - which join amino acids to form separate.
a polypeptide chain. - A replication fork is formed which serves as a
- rRNAs combine with proteins in the template for replication
cytoplasm to form ribosomes, which act Enzymes and Proteins involved:
as the site of protein synthesis and has DNA Helicase – The point at which the
the enzymes needed for the process. replication begins is known as the Origin of Replication.
- These complex structures travel along the DNA Helicase brings about the procedure of strand
mRNA molecule during translation and separation, which leads to the formation of the
facilitate the assembly of amino acids to form replication fork. It breaks the hydrogen bond between
a polypeptide chain. They bind to tRNAs and the base pairs to separate the strand. It uses energy
other molecules that are crucial for protein obtained from ATP Hydrolysis to perform the function.
synthesis. SSB Protein – Next step is for the Single-
Function: rRNA directs the translation of mRNA into Stranded DNA Binding Protein to bind to the single-
proteins.
stranded DNA. Its job is to stop the strands from Exons
binding again. - are nucleotide sequences in DNA and RNA that
DNA Primase – Once the strands are are conserved in the creation of mature RNA.
separated and ready, replication can be initiated. For - usually include both the 5’- and 3’-
this, a primer is required to bind at the Origin. RNA untranslated regions of mRNA, which contain
Primers are short sequences of RNA, around 10 start and stop codons, in addition to any protein
nucleotides in length. Primase synthesizes the primers. coding sequences.
2. Elongation - Can be considered as expressed sequences.
DNA Polymerase III - This enzyme makes the - Average of 8.8 exons per human gene.
new strand by reading the nucleotides on the template
strand and specifically adding one nucleotide after the
other.
- It can only synthesize new strands in the
direction of 5’ to 3’. It also helps in proofreading and
repairing the new strand.
- Main Replication Enzyme
Sliding Clamp - a ring-shaped protein that
The process by which DNA is used as a template to
holds the polymerase into position.
create mRNA is called transcription
Leading Strand – the strand, which is synthesized in
RNA Translation
the same direction as the replication fork.
RNA translation - is the process of protein synthesis
- The template for this strand runs in the
in which the genetic information encoded in mRNA is
direction of 5’ to 3’. The Polymerase has to
translated into a sequence of amino acids on a
attach only once and it can continue its work as
polypeptide chain.
the replication fork moves forward.
Process of Translation:
Lagging Strand - the strand being synthesized in the
1. Ribosomes bind to mRNA in the cytoplasm and
other direction (3’ to 5’)
move along the molecule in a 5’ – 3’ direction until it
- The polymerase has to synthesize one fragment
reaches a start codon (AUG)
of DNA. Then as the replication fork moves
2. Anticodons on tRNA molecules align opposite
ahead, it has to come and reattach to the new
appropriate codons according to complementary base
DNA available and then create the next
pairing (e.g. AUG = UAC). Each tRNA molecule carries a
fragment. These fragments are known as
specific amino acid (according to the genetic code)
Okazaki fragments (named after the scientist
3. Ribosomes catalyse the formation of peptide bonds
Reiji Okazaki who discovered them).
between adjacent amino acids (via condensation
reactions). The ribosome moves along the mRNA
3. Termination
molecule synthesising a polypeptide chain until it
DNA Polymerase I – It takes the help of
reaches a stop codon.
RNase H to remove the RNA primer and fill in the
4. At this point translation ceases and the polypeptide
gaps.
chain is released
Translation Mnemonic
DNA ligase – When Polymerase III is adding
The key components of translation are:
nucleotides to the lagging strand and creating Okazaki
 Messenger RNA (goes to…)
fragments, it at times leaves a gap or two between the
 Ribosome (reads sequence in …)
fragments. These gaps are filled by ligase.
 Codons (recognised by …)
- It also closes nicks in double-stranded DNA.
 Anticodons (found on …)
DNA Introns and Exons
 Transfer RNA (which carries …)
Introns and Exons - are nucleotide sequences
 Amino acids (which join via …)
within a gene.
 Peptide bonds (to form …)
Introns
 Polypeptides
- are nucleotide sequences in DNA and RNA that
DNA Cloning
do not directly code for proteins, and are
Clone is a genetically exact copy.
removed during the precursor messenger RNA
Gene Cloning -also known as molecular
(pre-mRNA) stage of maturation of mRNA by
cloning, refers to the process of isolating
RNA splicing.Can be considered as intervening
a DNA sequence of interest for the purpose of making
sequences
multiple copies of it. The identical copies are clones.
- can range in size from 10’s of base pairs to
1973 - Stanley Cohen and Herbert Boyer
1000’s of base pairs, and can be found in a wide
developed techniques to make recombinant DNA, a
variety of genes that generate RNA in most
form of artificial DNA. 
living organisms, including viruses.
- Recombinant DNA - is engineered through the
- Average 7.8 introns per human gene.
combination of two or more DNA strands,
 combining DNA sequences which would not damaged base forming an AP site which is
normally occur together. In other words, selected repaired by AP endonuclease before the
DNA (or the DNA of "interest") is inserted into an nucleotide gap in the DNA strand is filled by DNA
existing organismal genome, such as a bacterial polymerase.
plasmid DNA, or some other sort of vector. Nucleotide excision repair - is a widespread
- It can be inserted into another cell, such as a mechanism for repairing damage to DNA and
bacterial cell, for amplification and possibly recognizes multiple damaged bases.
production of the resulting protein. This process -  This mechanism is used to repair the formation
is called transformation, the genetic alteration of pyrimidine dimers from UV light within
of a cell resulting from the uptake, incorporation, humans.
and expression of foreign genetic material. - The process involves the recognition of damage
Recombinant DNA technology - was made which is then cleaved on both sides by
possible by the discovery of restriction endonucleases before resynthesis by DNA
endonucleases. polymerase.
DNA Repairing Mismatch repair – occurs when mismatched
Damage to DNA - is caused by the incorporation of bases are incorporated into the DNA strand during
incorrect nucleotide bases during DNA replication and replication and are not removed by proofreading DNA
the chemical changes caused by spontaneous mutation polymerase.
or exposure to environmental factors such as radiation. - In mismatch repair, the missed errors are later
The direct reversal DNA repair mechanism corrected by enzymes which recognize and
Direct reversal of DNA damage -is a excise the mismatched base to restore the
mechanism of repair that does not require a template original sequence.
and is applied to two main types of damage.
Direct reversal through photoreactivation LESSON 2: GENERAL PRINCIPLE OF DIGESTION
- UV light induces the formation of pyrimidine AND METABOLISM
dimers which can distort the DNA chain As you have learned, the process of mechanical
structure, blocking transcription beyond the area digestion is relatively simple. It involves the physical
of damage. breakdown of food but does not alter its chemical
- It can inverse this dimerization reaction by makeup. Chemical digestion, on the other hand, is a
utilizing light energy for the destruction of the complex process that reduces food into its chemical
abnormal covalent bond between adjacent building blocks, which are then absorbed to nourish the
pyrimidine bases. This type of photoreactivation cells of the body. In this section, you will look more
does not occur in humans. closely at the processes of chemical digestion and
The damage caused by alkylating agents absorption.
reacting with DNA The Process of Digestion
- This can also be repaired through direct reversal. 1. Digestion - large food molecules are broken
- Methylation of guanine bases produces a change down to smaller molecules, both mechanically
in the structure of DNA by forming a product that and chemically
is complimentary to thymine rather than 2. Absorption - process of transporting these
cytosine. smaller molecules across the intestinal wall
- The protein methyl guanine methyl 3. Elimination - undigested portions of food and
transferase (MGMT) can restore the original waste products are removed from the body
guanine by transferring the methylation product Figure 1. Digestion and Absorption. Digestion
to its active site. begins in the mouth and continues as food travels
DNA repair by excision through the small intestine. Most absorption occurs
Excision - is the general mechanism by which in the small intestine.
repairs are made when one of the double helix strands Chemical Digestion
is damaged. The non-defective strand is used as a Large food molecules (for example, proteins, lipids,
template with the damaged DNA on the other strand nucleic acids, and starches) must be broken down into
removed and replaced by the synthesis of new subunits that are small enough to be absorbed by the
nucleotides. lining of the alimentary canal. This is accomplished by
There are three types of excision repair enzymes through hydrolysis. The many enzymes
Base-excision repair involved in chemical digestion are summarized below.
Nucleotide excision repair. Enzymes from the salivary glands attack
Mismatch repair. carbohydrates (and fats in some species); enzymes
Base-excision repair - involves the recognition from the stomach attack proteins and fats; and
and removal of a single damaged base. enzymes from the exocrine portion of the pancreas
- The mechanism requires a family of enzymes attack carbohydrates, proteins, lipids, DNA, and RNA.
called glycosylases. The enzymes remove the Other enzymes that complete the digestive process are
found in the luminal membranes and the cytoplasm of polypeptides, which then travel to the small intestine
the cells that line the small intestine. The action of the (Figure 3). Chemical digestion in the small intestine is
enzymes is aided by the hydrochloric acid secreted by continued by pancreatic enzymes, including
the stomach and the bile secreted by the liver. chymotrypsin and trypsin, each of which act on specific
Carbohydrate Digestion bonds in amino acid sequences. At the same time, the
Glucose, galactose, and fructose are the three cells of the brush border secrete enzymes such
monosaccharides that are commonly consumed and as aminopeptidase and dipeptidase, which further
are readily absorbed. Your digestive system is also break down peptide chains. This results in molecules
able to break down the disaccharide sucrose, lactose, small enough to enter the bloodstream.
and maltose, and the polysaccharides glycogen and
starch. Your bodies do not produce enzymes that can Figure 4. Digestion of
break down most fibrous polysaccharides, such as Protein Flow Chart. Proteins
cellulose. While indigestible polysaccharides do not are successively broken
provide any nutritional value, they do provide dietary down into their amino acid
fiber, which helps propel food through the alimentary components.
canal.
The chemical digestion of starches begins in
Lipid Digestion
the mouth. In the small intestine, pancreatic amylase
A healthy diet
does the ‘heavy lifting’ for starch and carbohydrate
limits lipid intake to 35
digestion. After amylases break down starch into
percent of total calorie
smaller fragments, the brush border enzyme α-
intake. The most common
dextrinase starts working on α-dextrin, breaking off
dietary lipids are
one glucose unit at a time. Three brush border
triglycerides, which are
enzymes hydrolyze sucrose, lactose, and maltose into
made up of a glycerol molecule bound to three fatty
monosaccharides. Sucrase splits sucrose into one
acid chains. Small amounts of dietary cholesterol and
molecule of fructose and one molecule of glucose;
phospholipids are also consumed.
maltase breaks down maltose and maltotriose into two
The three lipases responsible for lipid digestion are
and three glucose molecules, respectively; and lactase
lingual lipase, gastric lipase, and pancreatic lipase.
breaks down lactose into one molecule of glucose and
However, because the pancreas is the only
one molecule of galactose. Insufficient lactase can lead
consequential source of lipase, virtually all lipid
to lactose intolerance.
digestion occurs in the small intestine. Pancreatic
lipase breaks down each triglyceride into two free fatty
acids and a monoglyceride. The fatty acids include
both short-chain (less than 10 to 12 carbons) and long-
chain fatty acids.
Nucleic Acid Digestion
The nucleic acids DNA and RNA are found in most of
the foods you eat. Two types of pancreatic
nuclease are responsible for their
digestion: deoxyribonuclease, which digests DNA,
and ribonuclease, which digests RNA. The nucleotides
produced by this digestion are further broken down by
two intestinal brush border enzymes
Figure 2. Carbohydrate Digestion Flow Chart. (nucleosidase and phosphatase) into pentoses,
Carbohydrates are broken down into their monomers in phosphates, and nitrogenous bases, which can be
a series of step absorbed through the alimentary canal wall. The large
food molecules that must be broken down into subunits
Figure 3. Digestion of Protein. The digestion of protein are summarized 
begins in the stomach and is completed in the small Absorbable Food Substances (Table 9)
intestine. Source & Substance
Carbohydrates Monosaccharides: glucose, galactose,
Protein Digestion and fructose
Proteins are polymers composed of amino Proteins S ingle amino acids, dipeptides, and
acids linked by peptide bonds to form long chains. tripeptides
Digestion reduces them to their constituent amino Triglycerides Monoacylglycerides, glycerol, and free
acids. You usually consume about 15 to 20 percent of fatty acids
your total calorie intake as protein. Nucleic acids Pentose sugars, phosphates, and
The digestion of protein starts in the stomach, where nitrogenous bases 4
HCl and pepsin break proteins into smaller Absorption
 The mechanical and digestive processes have All carbohydrates are absorbed in the form of
one goal: to convert food into molecules small enough monosaccharides. The small intestine is highly efficient
to be absorbed by the epithelial cells of the intestinal at this, absorbing monosaccharides at an estimated
villi. The absorptive capacity of the alimentary canal is rate of 120 grams per hour. All normally digested
almost endless. Each day, the alimentary canal dietary carbohydrates are absorbed; indigestible fibers
processes up to 10 liters of food, liquids, and GI are eliminated in the feces. The monosaccharides
secretions, yet less than one liter enters the large glucose and galactose are transported into the
intestine. Almost all ingested food, 80 percent of epithelial cells by common protein carriers via
electrolytes, and 90 percent of water are absorbed in secondary active transport (that is, co-transport with
the small intestine. Although the entire small intestine sodium ions). The monosaccharides leave these cells
is involved in the absorption of water and lipids, most via facilitated diffusion and enter the capillaries
absorption of carbohydrates and proteins occurs in the through intercellular clefts. The monosaccharide
jejunum. Notably, bile salts and vitamin B12 are fructose (which is in fruit) is absorbed and transported
absorbed in the terminal ileum. By the time chyme by facilitated diffusion alone. The monosaccharides
passes from the ileum into the large intestine, it is combine with the transport proteins immediately after
essentially indigestible food residue (mainly plant the disaccharides are broken down.
fibers like cellulose), some water, and millions of Protein Absorption
bacteria Active transport mechanisms, primarily in the
duodenum and jejunum, absorb most proteins as their
Fig 5 .Digestive Secretions and Absorption of Water. breakdown products, amino acids. Almost all (95 to 98
Absorption is a complex process, in which nutrients percent) protein is digested and absorbed in the small
from digested food are harvested. intestine. The type of carrier that transports an amino
acid varies. Most carriers are linked to the active
Absorption is achieved by the following mechanisms. transport of sodium. Short chains of two amino acids
1. Active transport (dipeptides) or three amino acids (tripeptides) are also
2. Facilitated transport. transported actively. However, after they enter the
3. Passive transport. absorptive epithelial cells, they are broken down into
their amino acids before leaving the cell and entering
Active transport the capillary blood via diffusion.
Active transport may be defined as the process of Lipid Absorption
solute movement from the lower concentration to the Absorption of fats occurs only in the small
higher concentration by the expense of energy. intestines. Once the triglycerides are broken down into
Electrolytes like Na ions are absorbed by active individual fatty acids and glycerols, along with
transport into the blood. cholesterol, they will aggregate into structures called
Facilitated transport micelles. Fatty acids and monoglycerides leave the
Facilitated transport is defined as the process of micelles and diffuse across the membrane to enter the
movement of solutes across the biological membrane intestinal epithelial cells. In the cytosol of epithelial
with the help of specific carrier proteins. Some cells, fatty acids and monoglycerides are recombined
digested amino acids and glucose are absorbed into back into triglycerides. In the cytosol of epithelial cells,
the blood by this method. triglycerides and cholesterol are packaged into bigger
Passive transport particles called chylomicrons which are amphipathic
Passive transport is defined as the process of solute structures that transport digested lipids. Chylomicrons
movement across a cell membrane without a will travel through the bloodstream to enter adipose
requirement of energy. After digestion, simpler food and other tissues in the body
substance is absorbed into the blood by passive
transport.
Some digested products from fats cannot be absorbed
into the blood. Example: Fatty acids and glycerol.
These components attach to micelles which are small
droplets and form the micelle-component complex.
This micelle – component complexes are re-formed into
chylomicrons. Chylomicrons are a small protein coated
fat globules. Then, chylomicrons move into the lymph
vessels and release the digested products into the
blood. Finally, the digested and absorbed products
reach the tissue to be utilized for their activities. This
process is called as assimilation.
Carbohydrate Absorption
 exception is vitamin B12, which is a very large
molecule. Intrinsic factor secreted in the stomach binds
to vitamin B12, preventing its digestion and creating a
complex that binds to mucosal receptors in the
terminal ileum, where it is taken up by endocytosis.
Water Absorption
Each day, about nine liters of fluid enter the
small intestine. About 2.3 liters are ingested in foods
and beverages, and the rest is from GI secretions.
About 90 percent of this water is absorbed in the small
intestine. Water absorption is driven by the
concentration gradient of the water: The concentration
of water is higher in chyme than it is in epithelial cells.
Thus, water moves down its concentration gradient
from the chyme into cells. As noted earlier, much of
the remaining water is then absorbed in the colon.

Metabolism
Once the food has been digested and
absorbed, the various nutrients are distributed to the
tissues via the blood and, having passed through the
Fig 6.
cell membranes, are exposed to the metabolic
Lipid Absorption. Unlike amino acids and simple sugars,
machinery of the cell. The purpose of this machinery is
lipids are transformed as they are absorbed through
(1) to release some of the energy contained in the
epithelial cells.
nutrients and convert it into a form that can be used
for the various functions of the cell, and (2) to use the
Nucleic Acid Absorption rest of the material for the synthesis of substances that
The products of nucleic acid digestion— the body needs for its growth and activities.
pentose sugars, nitrogenous bases, and phosphate ions In order to do this the food materials are
—are transported by carriers across the villus subjected to a variety of metabolic processes, each of
epithelium via active transport. These products then which involves a well-defined sequence of reactions.
enter the bloodstream. Nearly every step is catalysed by a different enzyme,
and results in a small but specific chemical change.
This field of intermediary metabolism constitutes a
Mineral Absorption
major part of biochemistry. The main metabolic
The electrolytes absorbed by the small
pathways have by now all been elucidated, and
intestine are from both GI secretions and ingested
metabolic maps prepared, which show the possible
foods. Since electrolytes dissociate into ions in water,
origins and fates of all the major cellular constituents.
most are absorbed via active transport throughout the
Broadly speaking, metabolism may be divided into
entire small intestine. During absorption, co-transport
three areas. (1) Catabolism. This deals with the
mechanisms result in the accumulation of sodium ions
breakdown of materials with the release of energy. In
inside the cells, whereas anti-port mechanisms reduce
the process, carbon dioxide and water are produced,
the potassium ion concentration inside the cells. To
but these are essentially by-products since it is the
restore the sodium-potassium gradient across the cell
energy liberated during their formation that the body
membrane, a sodium-potassium pump requiring ATP
requires, and rarely the carbon dioxide and water
pumps sodium out and potassium in.
themselves. (2) Anabolism covers the processes by
In general, all minerals that enter the intestine
which complex substances are built up from simple
are absorbed, whether you need them or not. Iron and
precursors, and this utilizes much of the energy
calcium are exceptions; they are absorbed in the
released during the course of catabolism. (3) Between
duodenum in amounts that meet the body’s current
the clearly defined anabolic and catabolic pathways
requirements, as follows
lies a central area of metabolism in which various
Vitamin Absorption
simple compounds are interconverted.
The small intestine absorbs the vitamins that
The pathways are said to be amphibolic since
occur naturally in food and supplements. Fat-soluble
they have a dual function (amphi = both) and provide
vitamins (A, D, E, and K) are absorbed along with
material which may be used either for synthesis or for
dietary lipids in micelles via simple diffusion. This is
breakdown. Amphibolic pathway, a biochemical
why you are advised to eat some fatty foods when you
pathway that serves both anabolic and catabolic
take fat-soluble vitamin supplements. Most water-
processes. An important example of an amphibolic
soluble vitamins (including most B vitamins and
pathway is the Krebs cycle which is also called Citric
vitamin C) also are absorbed by simple diffusion. An
acid cycle, which involves both the catabolism of Figure 25.3 A summary of the events that must occur
carbohydrates and fatty acids and the synthesis of before triacylglycerols can reach the bloodstream
anabolic precursors for amino-acid synthesis. All the through the digestive process.
metabolic pathways involve the uptake or release of TRIACYLGLYCEROL STORAGE AND MOBILIZATION
energy. Energy is required for: Most cells in the body have limited capability for
1. Chemical syntheses and the process of growth in storage of TAGs. However, this activity is the major
which complex, highly organized molecules are built function of specialized cell called adipocytes. An
and assembled from small molecular precursors. adipocyte is a triacylglycerol-storing cell. Adipose
2. The maintenance of the highly ordered structure of tissue is tissue contains large number s of adipocyte
the cell. cells , it is the largest cells in the body .
3. Transport and the movement of materials against a Use of TAGs stored in adiposed tissue for energy
concentration gradient, i.e. from a region of lower to production is triggered by several hormones, including
one of higher concentration. glucagon and epinephrine. Hormonal interaction with
4. Mechanical work, e.g. the contraction of muscles and adipose tissue membrane receptors stimulates
movement of cilia. production of cAMP from ATP inside the adipose cell.
Without the expenditure of energy, membranes and The cAmp activates Protein kinase A (pKA) is a protein
other cell structures would disintegrate and it is only the dependent on cyclic adenosine monophosphate
by the constant expenditure of energy that living (cAMP).
organisms are able to adapt continually to the Overall process of taping the body’s triacylglycerol
prevailing conditions. energy reserves (adipose tissue) for energy is called
triacylglycerol mobilization. Triacylglycerol
LESSON 3: GENERAL PRINCIPLE OF DIGESTION mobilization is the hydrolysis of triacylglycerols
AND METABOLISM stored in adipose tissue, followed by release into
OF LIPIDS bloodstream of fatty acids and glycerol produced.
LIPID METABOLISM Triacylglycerol energy reserves (fat reserves ) are
Digestion and Absorption of Lipids the human body’s major source of energy.
98% of total dietary lipids are triacylglycerols. Like all GLYCEROL METABOLISM
lipids, triacylglycerols are insoluble in water. The During triacylglycerol mobilization, one molecule of
chunning action of the stomach breaks up glycerol is produced for each triacylglycerol completely
triacylglycerol materials into small globules, or hydrolyzed. After entering into the bloodstream,
droplets, which float as a layer above the other glycerol travels to the liver or kidneys, where it is
component of swallowed food. The resulting material is converted, in a two steps process, to dihydroxyacetone
called chyme. phosphate.
Lipid digestion also begins in the stomach. Under the OXIDATION OF FATTY ACIDS
action of gastric lipase enzymes, hydrolysis of TAGs There are three parts to the process by which fatty
occurs. acids are broken down to obtain energy.
The arrival of chyme from the stomach triggers in the
small intestine, through the action of the hormone
cholecystokinin, the release of the bile stored in the
gallbladder. The bile which contains no enzyme, acts
as an emulsifier.
Pancreatic lipase, which hydrolyze ester linkages
between the glycerol and fatty acid units of the TAGs.
With the help of bile, the free fatty acids and 1. The fatty acid must be activated by binding to a
monoacylglycerols produced from hydrolysis are coenzyme A.
combined into tiny spherical droplets called micelles. 2. The fatty acid must be transported into the
A fatty acid micelles is a micelle in which fatty acids mitochondrial matrix by a shuttle mechanism.
and/or monoacylglycerols and some bile are present. 3. The fatty acid must be repeatedly oxidized, cycling
A chylomicron is a lipoprotein that transports through a series of four reaction, to produced acetyl
triacylglycerols from intestinal cells, via the lymphatic CoA, FADH2+ and NADH.
system, to the bloodstream. Triacylglycerols constitute FATTY ACID ACTIVATION
95% of the core lipids present in a chylomicron. The first step of fatty acid oxidation is activation. A CoA
Chylomicrons enter the lymphatic system through molecule is added to the fatty acid to produce acyl-
tiny lymphatic vessels in the intestinal lining. They CoA, converting ATP to AMP in the process. Note that in
enter the bloodstream through the thoracic duct, this step, the ATP is converted to AMP, not ADP. Thus,
where the fluid of the lymphatic system flows into a activation uses the equivalent of 2 ATP molecules4.
vein, joining the bloodstream.
 Under these conditions, the problem of inadequate
oxaloacetate supplies arises, which is compounded by
the body using oxaloacetate that is present to produce
glucose through gluconcogenesis.
Ketone body is produced from acetyl CoA when an
excess of acetyl CoA from fatty acid degradation
accumulates because of triacylglycerol-carbohydrate
metabolic imbalances. When oxaloacetate supplies are
too low for all acetyl CoA present to be processed
through the citric acid cycle, the excess acetyl CoA is
diverted to the formation of ketone bodies.

FATTY ACID TRANSPORT

Fatty acyl CoA is impermeable to the inner
mitochondrial membrane, so it is carried in the form of Chemically, these three structures are closely related.
fatty acyl carnitine. The relationship are most easily seen if the focus starts
Fatty acyl carnitine is transported across the inner with the molecule acetoacetate.
mitochondrial membrane in exchange for carnitine by 1. Reduction of the ketone group present in
an antiport translocase. acetoacetate to a secondary alcohol produces
In the mitochondrial matrix fatty acyl carnitine reacts betahydroxy-butyrate.
with CoA in a reaction catalyzed

by carnitine acyltransferase II (CAT-II), yielding fatty

acyl CoA and carnitine.

The fatty acyl CoA is now ready to undergo beta-

oxidation. Structurally, there is no ketone functional group
KETONE BODIES present in beta-hydroxybutyrate. Despite it not being a
ketone, it is called a ketone body because of its
structural relationship to acetoacetate.
2. Decarboxylation of acetoacetate produces acetone.

When there is adequate balance between lipid and Ketone bodies can serve as sources of energy for
carbohydrate metabolism, most of the acetyl CoA various tissues and are very important energy sources
produced from the beta-oxidation pathway is further in heart muscle and the renal cortex. Even the brain,
processed through the citric acid cycle. The first step of which requires glucose, can adapt to obtain a portion
the citric acid cycle involves the reaction between of its energy from ketone bodies in dieting situations
oxaloacetate and acetyl CoA. Sufficient oxaloacetate that involve a properly constructed low-carbohydrate
must be present for the acetyl CoA to react with. diet.
Oxaloacetate concentration depends on pyruvate Ketogenesis is the metabolic pathway by which
produced from glycolysis; pyruvate can be converted ketone bodies are synthesized from acetyl CoA. Even
to oxaloacetate by pyruvate carboxylase. when ketogenic conditions are not present in the
Certain body conditions upset the lipid-carbohydrate human body, the liver produces a small amount of
balance required for acetyl CoA generated by fatty ketone bodies.
acids to be processed by the citric acid cycle. Items to consider about this process prior to
These body conditions are: looking at the actual steps in this four-step
1. Dietary intake high in fat and low in carbohydrates process are:
2. Diabetic conditions where the body cannot 1. The primary site for the process is liver
adequately process glucose even though it is present mitochondria.
3. Prolonged fasting conditions, including starvation,
where glycogen supplies are exhausted.
2. The first ketone body to be produced is acetone on a person's breath; acetone is very volatile
acetoacetate. This production occurs in Step 3 of and is excreted through the lungs.
ketogenesis. 3. Some of acetoacetate produced in Step Symptoms of mild ketosis as a result of low-
3 is converted to the second ketone body, beta- carbohydrate diet include headache, dry mouth, and
hydroxybutyrate, in Step 4 of ketogenesis. sometimes foul-smelling breath.
4. The acetoacetate and beta-hydroxybutyrate Two of the three ketone bodies - acetoacetate and
synthesized by ketogenesis in the liver are released to beta-hydroxybutyrate are acids. Their presence in
the bloodstream where acetone, the third ketone body, blood causes a slight but significant decrease in blood
is produced. pH. This can result in acidosis in severe ketosis
5. Acetoacetate is somewhat unstable and can situations. Symptoms include heavy breathing
spontaneously or enzymatically lose its carboxyl group (because acidic blood can carry less oxygen) and
to form acetone. Thus, the ketone body acetone is not increased urine output that can lead to dehydration.
actually a product of the metabolic pathway Ultimately, the condition can cause coma and death.
ketogenesis. Acidosis from elevated ketone body levels is often
6. The ketone body acetone present in the bloodstream called keto acidosis or metabolic acidosis to
is a volatile substance that is mainly excreted by distinguish it from respiratory acidosis, which is not
exhalation. Its sweet odor is detectible in the breath of linked to ketone bodies.
a diabetic. Lipogenesis
7. The amount of acetone present is usually small Lipogenesis is a term used to describe a
compared to the concentration of the other two ketone process of fatty acid and triglyceride synthesis from
bodies. glucose or other substrates. This specific biosynthesis
Steps of ketogenesis: takes place predominantly in the liver, while its
Step 1: First condensation. Ketogenesis begins as two occurrence in the adipose tissue is of minor
acetyl CoA molecules combine to produce acetoacetyl significance.
CoA, a reversal of the last step of the beta-oxidation The Citrate-Malate Shuttle System
pathway. Acetyl CoA is the starting material for
Step 2: Second condensation. Acetoacetyl CoA then lipogenesis. Because acetyl CoA is generated in
reacts with a third acetyl CoA and water to produce 3- mitochondria and lipogenesis occurs in the cytosol, the
hydroxy-3-methylglutaryl CoA (HMG-CoA) and CoA--SH. acetyl CoA must first be transported to the cytosol. It
Step 3: Chain cleavage. HMG-CoA is then cleaved to exits the mitochondria through a transport system that
acetyl CoA and acetoacetate. involves citrate ion.
Step 4: Reduction. Acetoacetate is reduced to beta- The outer mitochondrial matrix is freely
hydroxybutyrate. The reducing agent is NADH. permeable to acetyl CoA, as well as many other
Energy Production from Acetoacetate substances such as citrate, malate and pyruvate. The
The ketone bodies beta-hydroxybutyrate and inner mitochondrial membrane, however, is not
acetoacetate are connected by a reversible reaction. permeable to acetyl CoA. An indirect shuttle system
Using a different enzyme than used in ketogenesis, involving citrate solves this problem.
beta-hydroxybutyrate can be converted back to Mitochondrial acetyl CoA reacts with
acetoacetate when cellular energy needs require it. oxaloacetate to produce citrate, which is then
For acetoacetate to be used a fuel, it must first be transported through the inner mitochondrial membrane
activated by transfer of a CoA group from succinyl CoA by a citrate transporter (a membrane protein
(a citric acid cycle intermediate). The resulting structure). Once in the cytosol, the citrate undergoes
acetoacetyl CoA is then cleaved to give two acetyl CoA the reverse reaction to its formation to regenerate the
molecules that can enter the citric acid cycle. In effect, acetyl CoA and oxaloacetate, with ATP involved in the
acetoacetate is a water-soluble, transportable form of process. The acetyl CoA so generated becomes the
acetyl units. “fuel” for lipogenesis; the oxaloacetate so generated
Ketosis reacts further to produce malate, in an NADH
Under normal metabolic conditions (an appropriate dependent change. The malate reenters the
glucose-fatty acid balance), the concentration of mitochondrial matrix through a malate transporter, and
ketone bodies in the blood is very low-about is then converted to oxaloacetate, which can then
1mg/100mL. Abnormal metabolic conditions produced react with another acetyl CoA molecule to form citrate
elevated blood ketone levels. Ketonemia is excess and the shuttle process repeats itself
accumulation of ketone bodies in blood (20mg/100mL). ACP Complex Formation
At a level of 70mg/100mL, the renal threshold is Two simple ACP complexes are needed to start
exceeded, and ketone bodies are excreted in the urine, the lipogenesis process. They are acetyl ACP and
a condition called ketonuria. The overall accumulation malonyl ACP.
of ketone bodies in the blood and urine is called Cytosolic acetyl CoA is the starting material for
ketosis. Ketosis is often detectable by the smell of the production of both of these simple ACP complexes.
Acetyl ACP is produced by the direct reaction of acetyl NADPH to mevalonate. This enzyme is the regulatory
CoA with an ACP molecule. enzyme of the pathway, and is inhibited by statins—the
The reaction to produce malonyl, ACP requires best lipid-lowering drugs. Mevalonate is
two steps . The first step is a carboxylation reaction phosphorylated by three kinases sequentially utilizing
with ATP involvement. three ATPs and is then decarboxylated to form
This reaction occurs only when cellular ATP isopentenyl diphosphate.
levels are high. It is catalyzed by acetyl CoA Isopentenyl diphosphate (5C) isomerizes to 3,3-
carboxylase complex, which requires both Mn2+ ion and dimethylallyl diphosphate (5C) by shifting a double
the B vitamin biotin for its activity. The malonyl CoA so bond and then condensation with isopentenyl
produced then reacts with ACP to produce malonyl diphosphate forms geranyl diphosphate (10C). Another
ACP. isopentenyl diphosphate molecule joins to form the
THE CHAIN ELONGATION 15C compound, farnesyl diphosphate. Two such 15C
Four reactions that occur in a cyclic pattern molecules fuse to form 30C squalene.
within the multienzyme fatty acids synthase complex Squalene is oxidized to squalene 2,3-epoxide by
constitute the chain elongation process used for fatty squalene epoxidase. During cyclization to lanosterol, a
acids. methyl group shifts from C14 to C13 and from C8 to
The reactions of the first turn of the cycle, in C14.
general terms The methyl groups on C14 and C4 are removed to form
STEP 1: CONDENSATION 14-desmethyl lanosterol and then zymosterol. The
Acetyl ACP and malonyl ACP condense together double bond at C8–C9 is subsequently shifted to C5–C6
to form acetoacetyl ACP. in two steps, forming desmosterol. The final step is the
STEP 2: FIRST HYDROGENATION reduction of the double bond of the side chain yielding
The Keto group of the acetoacetyl complex, a cholesterol molecule.
which involves the β-carbon atom, is reduced to the LESSON 4: GENERAL PRINCIPLE OF DIGESTION
corresponding alcohol by NADPH. AND METABOLISM
STEP 3. DEHYDRATION OF CARBOHYDRATE
The alcohol produced in STEP 2 is dehydrated Carbohydrates are organic molecules composed of
to introduce a double bond into the molecule (between carbon, hydrogen, and oxygen atoms. The family of
α and β carbons.) carbohydrates includes both simple and complex
STEP 4: SECOND HYDROGENATION sugars.
The double bond introduced in step 3 is Digestion is how your body turns food you eat into
converted to a single bond through hydrogenation. As nutrients it uses for energy, growth, and cell repair.
in step 2, NADPH is the reducing agent. Metabolism is a term that is used to describe all
Unsaturated Fatty Acid Biosynthesis chemical reactions involved in maintaining the living
Production of unsaturated fatty acids (insertion state of the cells and the organism. 
of double bonds) requires molecular oxygen (O 2). In an DIGESTION OF CARBOHYDRATES
oxidation step, hydrogen is removed and combined From the Mouth to the Stomach
with the O2 to form water. The mechanical and chemical digestion of
BIOSYNTEHESIS OF CHOLESTEROL carbohydrates begins in the mouth known as chewing
Cholesterol synthesis is an expensive process for (also known as mastication), crumbles the
cells in terms of energy. This pathway takes place in carbohydrate foods into smaller pieces. Saliva contains
cytoplasm. The liver and intestines are major the enzyme, a-salivary amylase, this enzyme catalyzes
contributors to endogenous production. Acetyl-CoA the hydrolysis of a-glycosidic linkages in starch from
units are joined to form a 30-carbon compound and plants and glycogen from meats to produce smaller
then three carbons are removed to produce cholesterol polysaccharides and the disaccharide maltose.
which has 27 carbon atoms. Only small amount of carbohydrate digestion occurs in
The cholesterol synthesis steps can be divided into: the mouth because food is swallowed so quickly.
1. Mevalonate synthesis 2. Isopentenyl phosphate Although the food remains longer in the stomach, very
synthesis little further carbohydrate digestion occurs there
3. Squalene formation 4. Lanosterol synthesis 5. either, because a-salivary amylase is inactivated by the
Cholesterol formation acidic environment of the stomach, and the stomach’s
Two acetyl-CoAs combine to form acetoacetyl-CoA, own secretions do not contain any carbohydrate-
releasing CoA-SH in the presence of thiolase. Acetyl- digesting enzymes. But the mechanical breakdown is
CoA also condenses to form 3-hydroxy-3- ongoing, the contractions of the stomach mix the
methylglutaryl-CoA (HMG-CoA) catalyzed by HMG-CoA carbohydrates into the more uniform mixture of
synthase. These enzymes are different from the chyme.
enzymes used for ketone body synthesis in From Stomach to Intestines
mitochondria. HMG-CoA is reduced by HMG-CoA The primary site for carbohydrate digestion is within
reductase using the small intestines, wherein upon entry of the chyme
in the upper small intestines, the a-amylase, this time glycogen, or glycogenolysis, which releases glucose
is secreted by the pancreas, again begins to function. and increases blood glucose levels.
The pancreatic a-amylase breaks down polysaccharide METABOLISM OF CARBOHYDRATES
chains into shorter segments until the disaccharide Carbohydrate metabolism begins with digestion in
maltose and glucose itself are the dominant species. the small intestine where monosaccharides are
The final step in carbohydrate digestion occurs on the absorbed into the blood stream. Blood sugar
outer membranes of intestinal mucosal cells, where the concentrations are controlled by three hormones:
enzymes that convert disaccharides to insulin, glucagon, and epinephrine.
monosaccharides are located. The important
disaccharide enzymes are:
1. Maltase - converts maltose into two glucose units
2. Sucrase - converts sucrose to one glucose and
one fructose unit
3. Lactase - converts lactose to one glucose and one
galactose unit
Absorption: To the Bloodstream
The three major breakdown products from
In the liver and muscles, most of the glucose is
carbohydrate from carbohydrate digestion are glucose,
changed into glycogen by the process
galactose and fructose. These monosaccharides are
of glycogenesis (anabolism). 
absorbed into the bloodstream through intestinal wall.
Anabolism occurs when smaller molecules such as
The folds of the of the intestinal wall are lined with
monosaccharides, amino acids and fatty acids are
fingerlike projections called villi. Absorption is by active
reformed into more complex molecules such as
transport. In this case ATP is needed. Protein carrier
glycogen, hormones, enzymes or whatever the body
mediate the passage of monosaccharides through cell
needs for growth and maintenance of cells and tissues.
membranes. After their absorption into the
Glycogen is stored in the liver and muscles until
bloodstream, monosaccharides are transported to the
needed at some later time when glucose levels are
liver.
low. If blood glucose levels are low, then eqinephrine
Maintaining Blood Glucose Levels: The Pancreas and
and glucogon hormones are secreted to stimulate the
Liver
conversion of glycogen to glucose. This process is
Glucose levels in the blood are tightly controlled, as
called glycogenolysis (catabolism).
having either too much or too little glucose in the blood
Catabolism begins with digestion and refers to the
can have health consequences. Glucose regulates its
breaking down of large, complex molecules into
levels in the
smaller molecules. Carbohydrates become
blood via a
monosaccharides, lipids become fatty acids and
process called
glycerol, and proteins become amino acids. Catabolism
negative
also occurs when old cells are broken down during
feedback.
maintenance and when energy is released during
Insulin-
intracellular catabolism.
secreting cells
(pancreatic
ATP (adenosine triphosphate) is referred to as the
beta cells) in
molecular “currency” of the cells. ATP is formed by the
the pancreas
catabolism of glucose, glycerol, fatty acids, and amino
sense the increase in blood glucose and release the
acids. It contains high-energy phosphate bonds that
hormonal message, insulin, into the blood. Insulin
release a significant amount of energy when ATP is
sends a signal to the body’s cells to remove glucose
broken down to ADP (adenosine diphosphate)
from the blood by transporting it into cells and within
and AMP (adenosine monophosphate). ATP is
the cell to use glucose to make energy. Insulin has an
regenerated by adding back phosphate groups through
opposing hormone called glucagon. Glucagon-secreting
the process of phosphorylation.
cells in the pancreas (pancreatic alpha-cells) sense the
drop in blood glucose and, in response, release the
hormone glucagon into the blood. Glucagon Metabolism consists of a series of chemical reactions
communicates to the cells in the body to stop using called metabolic pathways. The various metabolic
glucose. More specifically, it signals the liver to break pathways that occur take place in different parts of the
down glycogen and release the stored glucose into the cell, depending on the various enzymes contained in
blood, so blood glucose levels stay within the target those parts. The mitochondria often referred to as the
range and all cells get the fuel the need to function “powerhouse” of the cell contains the greatest number
properly. of metabolic enzymes and is the primary site where
Epinephrine or adrenaline is released in response to ATP is made.
stress or exercise. It causes the breakdown of Two chemical reactions involving water are
condensation and hydrolysis.
Condensation is typically an anabolic process which attached to the hydroxyl group of tyrosine of
combines smaller molecules into larger ones and water glyogenin. The first molecule of glucose is transferred
is released.  to glycogenin, which will then takes up for glucose
Hydrolysis on the other hand is usually catabolic and residues forming a fragment of primer. It will be the
involves breaking apart two molecules by adding a one to accept all glucose molecules.
water molecule.
Glycogen synthase transfers glucose from UDP-Glcose
GLCOLYSIS to glycogen (non-reducing end) forming alpha 1,4-
linkages.  The same enzyme catalyzes the synthesis of
the unbranched molecule with alpha-1,4-glycosidic
linkages.The final step is the formation of glycogen
branches caused by the effect of branching enzyme.
GLUCOGENESIS

Glycolysis is a series of reactions that extract energy

from glucose by splitting it into two three-carbon
molecules called pyruvates. Glycolysis takes place in
the cytosol of a cell, and it can be broken down into
two main phases: the energy-requiring phase and the
energy-releasing phase.
Energy-requiring phase in this phase, the starting
molecule of glucose gets rearranged, and two
phosphate groups are attached to it. The phosphate
groups make the modified sugar—now called fructose-
1,6-bisphosphate, allowing it to split in half and form
two phosphate-bearing three-carbon sugars.
Energy-releasing phase in this phase, each three-
carbon sugar is converted into another three-carbon
molecule, pyruvate, through a series of reactions. In
these reactions, two  ATP molecules and one  NADH
molecule are made.
In the second half of glycolysis, the three-carbon
sugars formed in the first half of the process go
through a series of additional transformations, Basically Gluconeogenesis is the reversal of Glycolysis.
ultimately turning into pyruvate. In the process, Glycolysis proceeds to another energy cycle called
four ATP molecules are produced, along with two Citric Acid Cycle by forming a substance
molecules of NADH called pyruvate.
<See photo> These 3 steps are circumvented by another set
of enzymes to form glucose at the end.
GLYCOGENESIS Substrates of Gluconeogenesis
In the initial phase, glucose is phosphorylated into  Glucogenic Amino Acids
Glucose-6-Phosphate, a usual reaction in glycolysis. It  Lactate
is catalyzed by glucokinase (liver) and
hexokinase (muscle). An enzyme
Phosphoglucomutase will catalyze the conversion
of Glucose-6-Phosphate and is converted to
Glcose-1-Phosphate.
Third step focuses on the reaction of Glucose-1-
Phosphate to UTP thereby forming active
nucleotide UDP-Glcose (Uridine Diphosphate
 Glycerol
Glucose). The one responsible for such reaction is the
 Fatty acid
enzyme UDPGlcose Pyrophosphorylase.
A small fragment of already existing glycogen will  Citric acid cycle
serve as a primer in order to stimulate the synthesis of
glycogen. The glucose from UDP-Glcose will be Glucogenic amino acid undergoes transamination
accepted by glycogenin. The initial glucose unit is which causes change in the carbon skeleton and
directly gets converted to pyruvate. Some Glucogenic
amino acids form oxaloacetic acid or other Glycogen phosphorylase stereoisomers (see
intermediates of Citric Acid Cycle. While alanine is photo)
preferred in liver, glutamine is preferred in kidney. Debranching enzyme is a single molecule consisting of
<see photo> 2 enzyme activities – α – [1→4]→α-[1→4] glucan
transferase and glucosidase. The first enzyme activity
Conversion of Glucogenic Amino Acids to removes the glycogen fragment containing 3 or 4
Pyruvate residues in a branch and move them to a nearby chain.
Muscular activities and anaerobic glycolysis in red This involves breaking up of 1→ 4 glycosidic link in one
blood cells produce a large amount of lactate. This point and the formation of the same at another point
lactate is taken up by the liver and gets converted to on the molecule.
pyruvate by the enzyme lactate dehydrogenase. The second enzyme activity breaks the 1→ 6 glycosidic
Pyruvate then gets converted to glucose by hepatic link at the branching point and release free glucose.
Gluconeogenesis which is then sent back to muscles Once the branching is lost, remaining linear fragment
for reuse. This is known as Cori Cycle. of glycogen is available for the action of phosphorylase
Cori Cycle in Liver and the process continues.

Action of Debranching enzyme

Formation of end products
The glycogen in the liver is used to increase the blood
glucose level when needed. The glycogen in muscle is
used to supply energy during muscle contraction as in
physical exercise and not to increase blood glucose.
The end products – glucose and glucose 1 phosphate
are formed by the combined action of the two
enzymes: debranching enzyme and gllycogen
phosphorylase.
The glucose 1 phosphate gets converted to glucose
Glycerol is formed by breaking down of triacylglecerol 6 phosphate by an enzyme Phosphoglucomutase. The
in the fatty tissue. It is then carried to the liver where it glucose 6 phosphate gets cleaved to glucose by
gets converted to Pyruvate and enters glucose 6 phosphatase which is present in liver, kidney
Gluconeogenesis.  and intestine.
Gluconeogenesis steps
 Gluconeogenesis starts either in mitochondria or
cytoplasm through a series of enzymatically
catalyzed steps.
 Glucose is converted to glucose 6 phosphate by
glucokinase/ hexokinase in glycolysis
 Fructose 1 phosphate is converted to fructose 6
phosphate in glycolysis by phosphorfructokinase
 Pyruvate is converted to phosphoenol pyruvate
by pyruvate kinase in glycolysis
 Rests are steps of Glycolysis in the opposite
direction towards glucose using the same
enzymes.

GLUCOGENOLYSIS Steps of glucogenolysis

Action of glycogen phosphorylase Stimulation of glucogenolysis
The key enzyme of glycogenolysis is glycogen A tight regulation of glycogenolysis is needed to keep
phosphorylase which is aided by another molecule the blood sugar under check. When the blood sugar
called pyridoxal phosphate. This enzyme cleaves the and the energy levels are low, glycogenolysis comes
glucose residues sequentially and yield glucose 1 into play. Glucagon and epinephrine are the hormones
phosphate. which are secreted in low blood sugar and when the
This cleavage is known as phosphorolysis which body is in distress. 
continues until 4 residues are present on either side of These hormones act through an intermediate molecule
a branching point. The resultant smaller and less called cAMP which is necessary for the activation of
branched glycogen molecule, limit dextrins. It cannot Glycogen phosphorylase. This mechanism is
be broken down further by Glycogen phosphorylase. commonly found in liver.
In muscles, only epinephrine causes effective Proteins are denatured in the stomach by the
glycogenolysis and in muscles, there is increased hydrochloric acid present in gastric juice. The acid
calcium inside the cells during muscle contraction . gives gastric juice a pH of between 1.5 and 2.0. The
This also results in activation of glycogen enzyme pepsin effects the hydrolysis of about 10% of
phosphorylase through a series of complicated peptide bonds in proteins, producing a variety of
reactions which does not involve camp. Epinephrine is polypeptides. In the small intestine, trypsin,
the hormone of fight, fright and  flight.  chymotrypsin, and carboxypeptidase in pancreatic
juice attack peptide bonds. The pH of pancreatic juice
LESSON 5: PROTEIN GENERAL PRINCIPLE OF is between 7.0 and 8.0, and it neutralizes the acidity of
DIGESTION AND METABOLISM the material from the stomach. Aminopeptidase,
Proteins is a large molecules composed of one or more secreted by intestinal mucosal cells, also attacks
chains of amino acids in a specific order determined by peptide bonds. Pepsin, trypsin, chymotrypsin,
the base sequence of nucleotides in the DNA coding for carboxypeptidase, and aminopeptidase are all
the protein. They are required for the structure, examples of proteolytic enzymes.
function, and regulation of the body's cells, tissues,
and organs. Each rotein has unique functions. Enzymes of this type are produced in inactive forms
There is protein in bones (collagen), muscles, and called zymogens that are activated at their site of
tendons; the hemoglobin that transports oxygen; and action.
enzymes that catalyze all biochemical reactions. The net result of protein digestion is the release of the
Protein is also used for growth and repair. Amid all protein’s constituent amino acid. Absorption of these
these necessary functions, proteins also hold the “free” amino acids through the intestinal wall requires
potential to serve as a metabolic fuel source. Proteins active transport with the expenditure of energy.
are not stored for later use, so excess proteins must be Different transport systems exist for the various kinds
converted into glucose or triglycerides, and used to of amino acids. After passing through the intestinal
supply energy or build energy reserves. Although the wall, the free amino acids enter the bloodstream,
body can synthesize proteins from amino acids, food is which distributes them throughout the body.
an important source of those amino acids, especially
because humans cannot synthesize all of the 20 amino PROTEIN METABOLISM
acids used to build proteins. AMINO ACID POOL
Amino acid, on absorption from intestine are
I. Body carried to liver through portal blood. They are taken up
by liver cells to extent and remainder enters the
Protein Digestion and Absorption systematic circulation and diffuse throughout the body
fluids and taken up by tissue cells.
Protein digestion begins in the stomach rather than in At the same time, most of the tissue proteins,
the mouth because saliva contains no enzymes that both structural and functional proteins including
affect proteins. Both protein denaturation and protein plasma proteins are continuously undergoing
hydrolysis occur in the stomach. The partially digested disintegration to release amino acid which enter the
protein (large polypeptides) passes from the stomach circulation. There is also a continues synthesis of
into the small intestine, where digestion is completed. nonessential amino acid.
Amino acids from all these sources get mixed
up to constitute an “amino acid pool” of the body. It
represents an availability of amino acid building units.

NITROGEN BALANCE
When the total amount of dietary nitrogen
absorbed from the alimentary canal, equals the total
amount of nitrogen eliminated from the body to urine,
sweat and gastrointestinal secretions, the body is in
nitrogen equilibrium with no change in its amount of
nitrogen. In this state, the rates of protein synthesis
and catabolism are identical in the body ordinarily,
normal healthy adults are in nitrogen equilibrium.

NEGATIVE NITROGEN BALANCE

Figure # 1 Summary of protein digestion in the human Negative nitrogen balance is the state where
body the nitrogen output exceeds its intake and there is a
consequent loss of nitrogen from the body. In other
words, the rate of protein catabolism exceeds that of
protein synthesis, resulting in a decline of tissue Transamination reaction
proteins. Wasting disease, surgical or medical trauma,
old age, protein malnutrition starvation and deficiency
of essential amino acids may cause a “negative
nitrogen balance”
Whenever some of the dietary nitrogen is
retained in the body a tissue protein, the intake of 2. Deamination
nitrogen exceeds its output from the body and is called
“positive nitrogen balance”. There is a rise in tissue
protein content because the rate of protein synthesis
exceeds that of protein catabolism, this happens
during growth, pregnancy and convalescence.

METABOLIC CLASSIFICATION OF AMINO ACIDS

1. Glycogenic Amino Acid
In amino acid metabolism, after the transfer of
amino group, remaining carbon skeleton containing
carbon, hydrogen and oxygen is oxidized like
carbohydrates and the intermediates may be It is a process by which N of amino acid is
converted into glucose by “gluconeogenesis”. These removed as NH3. It is of two types:
amino acids are called glycogenic amino acids. They a. Oxidative Deamination
are – glycine, alanine, serine, threonine, valine, b. Nonoxidative deamination
asparatic acid, glutamic acid, cysteine, cysteine, Oxidative deamination
methionine proline, hydroxyl proline, arginine and Is the mechanism by which amino group is
histidine. removed from the α-carbon to form a keto group and
free NH3. It is catalyzed by D- and L-amino acid
2. Ketogenic Amino Acid oxidases in liver, kidney and several other tissues.
They form acetate or acetoacetate, the
intermediates of fatty acid metabolism. They cause Nonoxidative Deamination
ketosis and ketonuria and called ketogenic amino There are certain amino acids, which can be
acids, e.g. leucine. nonoxidatively deaminated to for NH3, by specific
enzymes.
3. Glycogenic-ketogenic amino acids 1. Hydroxy amino acids such serine, threonine
Their carbon skeletons change partly to and homoserine undergo primary
glucose by glycogenesis and partly to ketone bodies, dehydration catalyzed by “amino acid
e.g. isoleucine, lysine, phenyl alanine, tyrosine, dehydrogenase”, which requires pyridoxal phosphate
tryptophan. as coenzymes; followed by spontaneous deamination.
2. Histidine is nonoxidatively deaminated by
METABOLISM OF AMINO ACID the specific enzyme histidase to form NH3 and
Nitrogen catabolism consists of removal of – urocanic acid.
NH2 groups of amino acids, converted to NH 3 and then 3. Sulfur containing amino acids such as
to urea and uric acid and is secreted in the urine. cysteine and homocysteine undergo desufhyydration
The remaining carbon skeletons may change to (removal of H2S) by desulfhydrases, forming an imino
glucose or ketone bodies, etc. acid then spontaneous deamination.

Metabolism of amino acids or formation of NH3 3. Transdeamination (Deamination of L-glutamic

and urea can be discussed under the following: Acid)
L-glutamic acid is deaminated by L-glutamate
1. Transamination dehydrogenase, which reuires NAD or NADP as
Is a reversible reaction in which α-NH2 group of coenzyme, but not by L-amino acid oxidase.
one amino acid is transferred to a α-keto acid resulting L-glutamate is converted to α-imino gluratic
formation of a new amino acid and a new keto acid. acid by L-glutamate dehydrogenase, which react with a
Donor amino acid becomes a new keto acid molecule of water to form NH3 and α-ketoglutarate.
after losing the α-NH2 group, and the recipient keto
acid becomes a new amino acid after receiving the α- 4. Ammonia Transport/Ammoinia Metabolism
NH2 group. The NH3 liberted by deamination, NH3
It is a process of combined deamination and produced in the lver, NH3 absorbed fro the intesine
amination. produced by intestinal flora action on the food; is not
allowed to accumulate but rapidly metabolized. Liver is
the main site of ammonia metabolism.m blood glutamine synthetase, and requires ATP. The reaction
ammonia is normally 10-12 ug/100 ml. increase in is irreversible.
blood ammonia is highly toxic to the CNS and may be
fatal. In liver diseases, there ay be increase in blood
ammonia levels with depression of the CNS, a condition
called hepaic coma.

5. Urea cycle (Krebs-Henseleit Cycle)

The removal of excess of NH3 derived from
amino acid catabolism is accomplished by the Glutamine synthetase occurs as "active" and "inactive,
production of urea which is excreted in the urine. Form. Active form is "deadenylated" and "inactive"
Urea formaton takes place manly in the liver form is adenylated". Thus glutamine synthetase is
and to a limited extent in kidneys and brain. The regulated by reversible adenylation and deadenylation.
enymes involved in urea formation are located in In brain, the major mechanism for removal of NH3 is
mitochondra and cytoplasm. glutamine formation and in the liver, the most
In urea cycle, one molecule or NH3 and one important pathway is urea formation. Glutamine is
molecule of CO2 are converted to one molecule of urea hydrolyzed to form NH3 in kidneys by renal
for each turn of the cycle and ornithin is regenerated ar glutarninase. NH3 production by the kidney is
the end, which acts as catalytic agent. The overall increased in metabolic acidosis and decreased in
process in each turn f cycle requires three molecules of alkalosis.
ATP.

The urea cycle is effectively controlled by N-acetyl

glutamic acid. It is formed by combination of acetyl
CoA and glutamic acid. When the amino acid levels are Animation of a-keto acids to form amino acids
high there is increased formation of N-acetyl glutamic
acid which stimulates carbamoyl phosphate
synthethase and drives the urea cycle forwards.
Formation of citruline
Ornithine reacts with carbamoyl phosphate to form
cirtulline, catalyzed by ornithine transcarbomoylase or
ornithine carbamoyl transferase. Creatine and creatinine metabolism or creatinine
Condensation of citrulline with aspartate synthesis
Citrulline condenses with aspartate to form Creatine
arginosuccinate catalyzed by arginosuccinate Creatine is a normal constituent of the body. It is
synthetase. The reaction requires ATP. present in muscle brain, liver, testes and in blood. It
Cleavage of arginosuccinate can occur in free form and also as "phosphorylated
Cleavage of arginosuccinate to arginine and fumarate form", called as creatine-Pnosphate or phosphocreatine
is catalyzed by arginosuccinase or arginosuccinate or phosphagen. The total amount in adult human body
lyase. Urea cycle is directly coupled to energy is approx. 120 gm, Ninety eight percent of total
production. The fumarate can be converted to malic amount is present in muscles
acid and then to oxaloacetate in the Krebs cycle. The Creatinine
oxaloacetate on amination form aspartic acid again. Creatinine is the anhydride of creatine, and it is in this
Cleavage of arginine form that creatine is excreted in urine in normal health.
Cleavage of arginine to ornithine and urea is catalyzed Formation of creatinine is a prerequisite for excretion
by arginase, which is present only in the liver. The of most of creatine, creatinine is excreted in males 1.5
enzyme requires cobalt and Mn— ions as activator. to 2.0 gm in 24 hours urine, and in females 0.8-1.5 gm
This reaction completes the urea cycle and in 24 hours urine.
regenerates ornithine. Blood urea Normal individual Synthesis of creatine
has a blood urea of 15 to 40 Mg/ 100 ml. Urea is mainly Creatine is synthesized in liver and kidney from three
excreted by the kidney. It is freely Permeable through amino acids, glycine, argenine and methathione.
the glomerulus but a portion is reabsorbed by the renal 1. The first reaction in creatine synthesis is that of
tubule and the rest excreted. The urea clearance value trans-amination of amidine group from arginine
is about 75 ml/min. When urine formation is 2 ml/min to glycine to form "guanidoacetic acids, also
or more. called "glycocyamine. Catalyzed by arginine-
Glutamine formation glycine transamidinase. It takes place in
Increased NH3 concentration also increases glutamine kidney.
synthesis from glutamic acid. It is catalyzed by 2. Glycocyamine is methylated to form creatine
phosphate. Active methionine (S-adenosyl
 methionine) is the methyldonor. This reaction
is catalyzed by guanidoacetate methylferase.
This reaction is irreversible and occur in liver,
creatine phosphate is mainly stored in muscles.
3. creatine phosphate in muscles, converted into
Creatinine, which is nonenzymatic and
irreversible.