UNIT – 1 BIOCHEMISTRY OF LIFE

STRUCTURE OF PROTEINS

Primary Structure of Proteins

The sequence of amino acids in a protein is called the primary structure of the protein. In proteins, amino
acids are joined covalently by peptide bonds, which are amide linkages between the α-carboxyl group of one
amino acid and the α-amino group of another.

Secondary Structure of Proteins

The polypeptide backbone does not assume a random three-dimensional structure, but instead generally forms
regular arrangements of amino acids that are located near to each other in the linear sequence. These
arrangements are termed the secondary structure of the polypeptide. The α-helix, β-sheet, and β-bend (β-turn)
are examples of secondary structures frequently encountered in proteins.

α-Helix

It is a spiral structure, consisting of a tightly packed, coiled polypeptide backbone core, with the side chains
of the component amino acids extending outward from the central axis to avoid interfering sterically with each
other. A very diverse group of proteins contains α-helices. For example, the keratins are a family of closely
related, fibrous proteins whose structure is nearly entirely α-helical. An α-helix is stabilized by extensive
hydrogen bonding between the peptide-bond carbonyl oxygens and amide hydrogens that are part of the
polypeptide backbone. The hydrogen bonds extend up and are parallel to the spiral. All the peptide bond
components except the first and last are linked to each other through intrachain hydrogen bonds. Hydrogen
bonds are individually weak, but they collectively serve to stabilize the helix. Each turn of an α-helix contains
3.6 amino acids.
β-Sheet

The β-sheet is another form of secondary structure in which all of the peptide bond components are involved
in hydrogen bonding. The surfaces of β-sheets appear “pleated,” and these structures are, therefore, often
called “β-pleated sheets”. β-sheets are composed of two or more peptide chains (β-strands), or segments of
polypeptide chains, which are almost fully extended. Note also that in β-sheets the hydrogen bonds are
perpendicular to the polypeptide backbone. A β-sheet can be formed from two or more separate polypeptide
chains or segments of polypeptide chains that are arranged either antiparallel to each other (with the N-terminal
and C-terminal ends of the β-strands alternating), or parallel to each other (with all the N-termini of the β-
strands together). When the hydrogen bonds are formed between the polypeptide backbones of separate
polypeptide chains, they are termed interchain bonds. A β-sheet can also be formed by a single polypeptide
chain folding back on itself. In this case, the hydrogen bonds are intrachain bonds.
β-Bends

β-Bends reverse the direction of a polypeptide chain, helping it form a compact, globular shape. They are
usually found on the surface of protein molecules, and often include charged residues. β-Bends often connect
successive strands of antiparallel β-sheets.

Super secondary structures (motifs)

Super secondary structures are usually produced by packing side chains from adjacent secondary structural
elements close to each other. Thus, for example, α-helices and β-sheets that are adjacent in the amino acid
sequence are also usually (but not always) adjacent in the final, folded protein.

Some common structural motifs combining α-helices and/or β-sheets.

Tertiary Structure of Proteins

“Tertiary” refers both to the folding of domains (the basic units of structure and function), and to the final
arrangement of domains in the polypeptide. Domains are the fundamental functional and three-dimensional

structural units of polypeptides. Polypeptide chains that are greater than 200 amino acids in length generally
consist of two or more domains. The core of a domain is built from combinations of super secondary structural
elements (motifs). Four types of interactions cooperate in stabilizing the tertiary structures of proteins.

Disulfide bonds: A disulfide bond is a covalent linkage formed from the sulfhydryl group (–SH) of
each of two cysteine residues.

Hydrophobic interactions: Amino acids with nonpolar side chains tend to be located in the interior of
the polypeptide molecule, where they associate with other hydrophobic amino acids.

Hydrogen bonds: Amino acid side chains containing oxygen- or nitrogen-bound hydrogen, such as in
the alcohol groups of serine and threonine, can form hydrogen bonds with electron-rich atoms, such as the
oxygen of a carboxyl group or carbonyl group of a peptide bond. Formation of hydrogen bonds between polar
groups on the surface of proteins and the aqueous solvent enhances the solubility of the protein.
 Ionic interactions: Negatively charged groups, such as the carboxylate group (–COO–) in the side chain
of aspartate or glutamate, can interact with positively charged groups, such as the amino group (–NH3+) in the
side chain of lysine.

Quaternary Structure of Proteins

Many proteins consist of a single polypeptide chain, and are defined as monomeric proteins. However, others
may consist of two or more polypeptide chains that may be structurally identical or totally unrelated. The
arrangement of these polypeptide subunits is called the quaternary structure of the protein. Subunits are held
together by noncovalent interactions (for example, hydrogen bonds, ionic bonds, and hydrophobic
interactions). Subunits may either function independently of each other, or may work cooperatively, as in
haemoglobin, in which the binding of oxygen to one subunit of the tetramer increases the affinity of the other
subunits for oxygen.

COMPOSITION OF NUCLEOTIDES

Nucleotide essentially consists of base, sugar and phosphate. The term nucleoside refers to base+ sugar. A
nucleotide is nucleoside + phosphate. The nitrogenous bases found in nucleotides are aromatic heterocyclic
compounds. The bases are of two types-purines and pyrimidines. Purines are numbered in the anticlockwise
direction while pyrimidines are numbered in the clockwise direction.

General Structure of Purines

General Structure of Pyrimidines

DNA and RNA contain the same purines namely adenine (A) and guanine (G). Further, the pyrimidine cytosine
(C) is found in both DNA and RNA. However, the nucleic acids differ with respect to the second pyrimidine
base. DNA contains thymine (T) whereas RNA contains uracil (U).
The five carbon monosaccharide (pentoses) are found in the nucleic acid structure. RNA contains D-ribose
while DNA contains D-deoxyribose. Ribose and deoxyribose differ in structure at C2. Deoxyribose has one
oxygen less at C2 compared to ribose.
STRUCTURE OF DNA

The double helical structure of DNA was proposed by lames Watson and Francis Crick in 1953 (Nobel Prize,
1962). The structure of DNA double helix is comparable to a twisted ladder. The salient features of Watson-
Crick model of DNA (now known as B-DNA) are given below:

1. The DNA is a right-handed double helix. Lt consists of two polydeoxyribonucleotide chains (strands)
twisted around each other on a common axis.

2. The two strands are antiparallel, i.e., one strand runs in the 5'to 3'direction while the other in 3' to 5' direction.

3. The width (or diameter of a double helix ls 20 A° (2 nm).

4. Each turn (pitch) of the helix is 34 A° (3.4 nm) with 10 pairs of nucleotides, each pair placed at a distance
of about 3.4 A°.

5. Each strand of DNA has a hydrophilic deoxyribose phosphate backbone (3'-5' phosphodiester bonds) on the
outside (periphery) of the molecule while the hydrophobic bases are stacked inside (core).

6. The two polynucleotide chains are not identical but complementary to each other due to base pairing.

7. The two strands are held together by hydrogen bonds formed by complementary base pairs. The AT pair has
2 hydrogen bonds while CG pair has 3 hydrogen bonds. The CG bond is stronger by about 50% than AT bond.

8. The hydrogen bonds are formed between a purine and a pyrimidine only. If two purines face each other,
they would not fit into the allowable space. And two pyrimidines would be too far to form hydrogen bonds.
The only base arrangement possible in DNA structure, from special consideration is A-T, T -A, C-G and G-C.
9. The complementary base pairing in DNA helix proves Chargaff's rule. The content of adenine equals to that
of thymine (A = T) and guanine equals to that of cytosine (G = C).

10. The genetic information resides on one of the two strands known as template strand or sense strand. The
opposite strand is antisense strand The double helix has (wide) major grooves and (narrow) minor grooves
along the phosphodiester backbone. Proteins interact with DNA at these grooves, without disrupting the base
pairs and double helix.

TYPES OF RNA AND THEIR FUNCTIONS

VITAMINS
PHOSPHOLIPIDS
 Unit – 2 THE CELL
Cell Organelles
• Cell Membrane • Mitochondria
• Nucleus • Lysosomes
• Cell Wall • Peroxisomes
• Cytoplasm • Cilia and Flagella
• Cytoskeleton • Basal Bodies
• Ribosomes • Centrioles
• Endoplasmic Reticulum • Vacuoles
• Golgi Apparatus • Plastids

ROLE OF CELL ORGANELLES

Plasma Membrane: A lipid-protein-carbohydrate complex, providing a barrier and containing transport and
signaling systems.

Nucleus: Double membrane surrounding the chromosomes and the nucleolus. Pores allow specific
communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome.

Mitochondria: Surrounded by a double membrane with a series of folds called cristae. Functions in energy
production through cellular respiration and metabolism. Contains its own DNA, and is believed to have
originated as a captured bacterium.

Chloroplasts (plastids): Surrounded by a double membrane, containing stacked thylakoid membranes.

Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars. Contains DNA, and
like mitochondria, is believed to have originated as a captured blue-green algae. They are present only in
plants.

Rough endoplasmic reticulum (RER): A network of interconnected membranes forming channels within
the cell. Covered with ribosomes (causing the “rough” appearance), which are in the process of synthesizing
proteins for secretion or localization in membranes.

Smooth endoplasmic reticulum (SER): A network of interconnected membranes forming channels within
the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals
including drugs and pesticides.

Ribosomes: Protein and RNA complex responsible for protein synthesis.

Golgi apparatus: A series of stacked membranes. Vesicles (small membrane surrounded by bags) carry
materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are
“processed” to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final
destinations including secretion or membrane localization.
Lysosymes: A membrane-bound organelle that is responsible for degrading proteins and membranes in the
cell, and also helps degrade materials ingested by the cell.

Vacuoles: Membrane surrounded “bags” that contain water and storage materials in plants.

Peroxisomes or Microbodies: Produce and degrade hydrogen peroxide, a toxic compound that can be
produced during metabolism.

Cell wall: Plants have a rigid cell wall in addition to their cell membranes. It is absent in animals.

MITOCHONDRIA

Mitochondria are another very important membrane-bound organelle present in both animal and plant cells.
Mitochondria are the powerhouse of cells as they generate energy for cell functioning. They are short
cylindrical structures. There are two membranes covering this organelle, an outer membrane and an inner
membrane with a space in between. The inner membrane has a number of infoldings into the matrix known
as cristae. The matrix of mitochondria contains 70S ribosomes and a circular DNA in addition to a large
number of enzymes. On the surfaces of the cristae there are a large number of granular structures known as
oxysomes. The main function of mitochondria is that they are the centers of powergeneration inside the cells.
Functions of mitochondria include: ATP or energy production, immunity regulation, calcium balance, cell
death and renewal (autophagy), stem cell regulation. The final stage of respiration, the cellular respiration,
takes place in mitochondria. Cellular respiration or the oxidative breakdown of glucose occurs in three steps
– glycolysis, Kreb’s cycle and electron transport system and oxidative phosphorylation (synthesis of ATP).
The site of glycolysis is outside the mitochondria in the cytoplasm. The other two steps take place inside the
mitochondria. The site of Krebs cycle is in the matrix and that of ETS is on the inner side of the cristae.

STAGES OF CELL GROWTH

1. G1 phase: primary growth phase. Cell does its housekeeping activities. The period between M-phase and
S-phase is called G1 phase.

2. S-phase: DNA replication.

3. G2 phase: chromosome condensation, cell organelle replication.
4. M-phase: mitosis (nuclear division) (prophase, metaphase, anaphase, and
telophase).
5. C phase: cytokinesis (cytoplasmic division), daughter cells form.
MITOSIS
Mitosis is the process that facilitates the equal partitioning of replicated chromosomes into two identical
groups. Two new daughter cells arise from one original cell. All the cells created through mitosis are
genetically identical to one another and to the cell from which they came. The main purpose of mitosis in
eukaryotic cells is:

Growth of the individual,

To repair tissue, and
To reproduce asexually.
Mitosis is divided into four stages—prophase, metaphase, anaphase, and telophase. The important changes
that the cells undergo in each phase are described below.

Prophase

During prophase the nuclear membrane and nucleolus disappear. The chromosomes themselves condense from
long, thin filaments into compact rods so that they can be more easily moved. The apparatus needed to move
the chromosomes around is set up. In animal cells this is done by the two centrioles, which move toward
opposite poles of the cell and begin to form the mitotic spindle. Plant cells do not have centrioles; they use a
different mechanism to form the spindle fibers. Each chromosome has a spindle fiber attached to it at the
centromere and extending off to either side of the cell where the centrioles are located. These spindle fibers
are exerting tension on the chromosomes and when the centromere splits later on, this will allow the
chromosomes to be pulled to either end of the cell.

Metaphase

Metaphase is an easy stage to recognize because all of the chromosomes are lined up at the equator of the cell.

Anaphase

In anaphase the centromere on each chromosome splits. Because the spindle fibers are exerting tension on the
chromosomes, when the centromere splits each chromatid is pulled toward the spindle pole that it faces. Once
a chromatid has its own centromere it can be called a chromosome.

Telophase

In telophase the chromosomes reach the opposite poles of the cell and their attached spindle fibers disappear.
A new nuclear envelope forms, the nucleolus reappears, and the condensed chromosomes expand once more.
The cytoplasm divides in a process called cytokinesis, and this forms the two daughter cells. In animal cells
the cell membrane pinches in from either side by a constriction and separates into two. In a plant, a new cell
wall begins to form in the middle of the cell and gradually grows longer from each end as it works its way
toward the edges of the cell. Mitosis is finished and there now are two cells, which are identical to eachother,
and identical to the cell from which they came.

MEIOSIS

Meiosis is a cell division process where a single (parent) cell divides twice to produce four independent
(daughter) cells, each having half the chromosomes as the original cell. Meiosis is a type of cell division that
reduces the chromosome number by half (2n to n), leading to the formation of four non-identical daughter
cells. Meiosis takes place only in the reproductive cell types (sperm and egg cells) of sexually reproducing
organisms, including humans. For a cell to undergo meiosis, it must have a diploid (2n) chromosome number.

Meiosis involves two successive stages or phases of cell division, meiosis I and meiosis II. Each stage includes
a period of nuclear division or karyokinesis and a cytoplasmic division or cytokinesis. Although not a part of
meiosis, the cells before entering meiosis I undergo a compulsory growth period called interphase.

Meiosis I

Cells enter meiosis from interphase, which is much like interphase in mitosis (the cell cycle). When cells
commit to meiosis, DNA replicates. In humans, there are 46 chromosomes or 46 pairs of chromatids. Outside
of the nucleus, microtubules extends from two centrosomes, each with a pair of centrioles.
Prophase I

This is the longest phase of meiosis. Chromosomes condense and become visible. Homologous chromosomes
(chromosomes with the same genes but possibly different versions of those genes) come together in pairs in a
process called synapsis, forming tetrads. Crossing-over, or genetic recombination, occurs, where sections of
chromatids from one chromosome exchange places with sections from its homologous chromosome. This
creates genetic diversity. The nuclear envelope begins to dissolve, and spindle fibers form.

Metaphase I

Tetrads (pairs of homologous chromosomes) line up at the metaphase plate in the center of the cell. Spindle
fibers attach to the centromeres of each homologous chromosome.

Anaphase I

Spindle fibers pull the homologous chromosomes apart, moving them to opposite poles of the cell. Unlike
mitosis, the sister chromatids remain attached and do not separate.

Telophase I

The separated chromosomes reach the opposite poles, and the nuclear envelope starts to reform around them.
The cell then undergoes cytokinesis, dividing the cytoplasm and producing two daughter cells, each with half
the original chromosome number (haploid).

Meiosis II

Meiosis II is similar to mitosis but involves the division of haploid cells. It consists of the following stages:

Prophase II

Chromosomes condense and become visible again. The nuclear envelope dissolves, and spindle fibers begin
to form. At this stage, each cell has a haploid number of chromosomes (in humans, 23 chromosomes or 23
pairs of chromatids).

Metaphase II

Chromosomes line up at the metaphase plate in the center of the cell. Spindle fibers attach to the centromeres
of each chromosome.

Anaphase II

Sister chromatids finally separate and are pulled to opposite poles of the cell by the spindle fibers.

Telophase II

Chromatids reach the opposite poles, and the nuclear envelope reforms around them. Cytokinesis occurs,
resulting in four non-identical haploid daughter cells.
 Unit – 3 THE TISSUE

TISSUE AND ITS CLASSIFICATION

A group of cells that are similar in structure and work together to achieve a particular function forms a tissue.

There are four basic tissue types defined by their morphology and function:

• Epithelial tissue
• Connective tissue
• Muscle tissue
• Nervous tissue

Epithelial tissue creates protective boundaries and is involved in the diffusion of ions and molecules.
Epithelium forms the coverings of surfaces of the body. As such, it serves many purposes, including protection,
adsorption, excretion, secretion, filtration, and sensory reception. Is commonly called covering and lining
tissue.

Connective tissue underlies and supports other tissue types. Connective tissue is the most abundant and
widely distributed tissue type found in the human body. The role of connective tissue is to protect, support,
and bind together parts of the body.

Muscle tissue contracts to initiate movement in the body. The cells that form muscle tissue have the unique
capability to shorten or contract to generate movement of the bodily components. This tissue is extremely
dense with cells and has many of blood channels.

Nervous tissue transmits and integrates information through the central and peripheral nervous systems. The
primary tissue of our nervous system is called nervous or nerve tissue. The body's functions are monitored
and regulated. Two types of cells are present in the nervous tissue: Nerve cells, often known as neurons, and
Glial cells, which nourish neurons and aid in the nerve impulses.
NERVOUS TISSUE

• Nervous tissue is composed of cells called nerve cells or neuron.

• Nerve cells are highly specialized for being stimulated and then transmitting the stimulus very rapidly
from one place to another within the body.
• The brain and spinal cord are composed of nervous tissue.
• Nerve cells live long, cannot be divided and replaced (except memory cell).
• The CNS and PNS of the nervous system are made up of nerve tissue, which has two different types
of cells called neurons and glial cells, as well as dendrites, cell bodies, axons, and nerve endings.
• Each neuron has three parts- Cyton / Cell body, Dendrites and axon.

Cyton: It has large central nucleus and cytoplasm from which long thin hair-like parts arise.

Dendrite: The short-branched fibre of neuron which receives nerve impulse.

Axon: A single long conducting fibre extending from a neuron that transmits impulse away from the cell body.

Functions of nervous tissue:

• Functions of tissues: Secretion, movement, strength, excretion, communication.

• Controls all body activities.
• It coordinates among various body parts during any body function.
• Dendrite carries nerve impulse towards the cyton whereas axon carry nerve impulse away from the
cyton.
• Synapse: It is the junction or region of union of axon of one neuron with the dendrite of another through
which nerve impulse are transferred.
EPITHELIAL TISSUE
The epithelial tissue covers the surface and lines tubes and cavities thus covers or protects the organs in the
animal body. Is commonly called covering and lining tissue.

Characteristics features:
• Cells are tightly packed and form continuous sheet.
• They have only small amount of connecting material between them and almost no intercellular space.
• All epithelium usually separated from the underlying tissue by an extracellular fibrous basement
membrane
• A vascular tissue lacking distribution of blood vessels.

Depending upon the space & function of the cells, the epithelial tissue is classified as follows:
Simple epithelial tissue:
Squamous epithelium / pavement epithelium:
• Cells are extremely thin & fat and form a delicate lining.
• Lining of oesophagous, lining of mouth, lining of blood vessels, lining of alveoli of lungs, lining of
Bowmans capsule of Nephron.

Cuboidal epithelium:
• Cells are cube shaped.
• Forms the lining of kidney tubule and ducts of salivary gland.

Columnar epithelium: (columnar= pillar like)

• It consists of tall cells.
• It is found in the inner lining of intestine where absorption and secretion occurs. This facilitates the
movement across the epithelial barrier.
• The cells of columnar epithelium modified to three types of epithelia:
▪ Ciliated epithelium
▪ Glandular epithelium
▪ Sensory epithelium

Complex epithelial tissue:

Stratified squamous epithelium: Skin epithelial cells are arranged in many layers to prevent wear and tear.
Since they are arranged in a pattern of layers the epithelium is called Stratified squamous epithelium.
 Unit 4 – Body Environment & Control

Anatomy deals with the structure of the body and its parts; in other words, the names of the parts. Physiology
studies the functions of these parts.

Homeostasis

The tendency to maintain a stable, relatively constant internal environment is called homeostasis. The body
maintains homeostasis for many factors in addition to temperature. For instance, the concentration of various
ions in your blood must be kept steady, along with pH and the concentration of glucose. If these values get
too high or low, you can end up getting very sick.

Homeostasis is maintained at many levels, not just the level of the whole body as it is for temperature. For
instance, the stomach maintains a pH that's different from that of surrounding organs, and each individual cell
maintains ion concentrations different from those of the surrounding fluid. Maintaining homeostasis at each
level is key to maintaining the body's overall function.

Homeostasis is regulated through control systems which have receptors (sensors), a set point, and effectors in
common.

a. Receptors are of many types whose job is to monitor for changes

b. The set point is the normal value or range of values

c. Effectors are muscles or glands that respond to the changes to return to stability

Negative Feedback Mechanism:

Maintenance of homeostasis usually involves negative feedback loops.

Example 1: First, high temperature will be detected by sensors—primarily nerve cells with endings in your
skin and brain—and relayed to a temperature-regulatory control center in your brain. The control center will
process the information and activate effectors—such as the sweat glands—whose job is to oppose the stimulus
by bringing body temperature down.
Example 2: In a healthy person, blood sugar levels are controlled by two hormones: insulin and glucagon.
Insulin decreases the concentration of glucose in the blood. After you eat a meal, your blood glucose levels
rise, triggering the secretion of insulin from β cells in the pancreas. Insulin acts as a signal that triggers cells
of the body, such as fat and muscle cells, to take up glucose for use as fuel. Insulin also causes glucose to be
converted into glycogen—a storage molecule—in the liver. Both processes pull sugar out of the blood,
bringing blood sugar levels down, reducing insulin secretion, and returning the whole system to homeostasis.

Glucagon does the opposite: it increases the concentration of glucose in the blood. If you haven’t eaten for a
while, your blood glucose levels fall, triggering the release of glucagon from another group of pancreatic cells,
the α cells. Glucagon acts on the liver, causing glycogen to be broken down into glucose and released into the
bloodstream, causing blood sugar levels to go back up. This reduces glucagon secretion and brings the system
back to homeostasis.
Positive Feedback Mechanism

Homeostatic circuits usually involve negative feedback loops. Some biological systems, however, use positive
feedback loops. Unlike negative feedback loops, positive feedback loops amplify the starting signal. Positive
feedback loops are usually found in processes that need to be pushed to completion, not when the status quo
needs to be maintained.

Example: A positive feedback loop comes into play during childbirth. In childbirth, the baby's head presses
on the cervix—the bottom of the uterus, through which the baby must emerge—and activates neurons to the
brain. The neurons send a signal that leads to release of the hormone oxytocin from the pituitary gland.

Oxytocin increases uterine contractions, and thus pressure on the cervix. This causes the release of even more
oxytocin and produces even stronger contractions. This positive feedback loop continues until the baby is
born.
ANTOMICAL PLANES AND DIRECTIONAL TERMS

Directional Terms

Directional terms describe the positions of structures relative to other structures or locations in the body.

Superior or cranial - toward the head end of the body; upper (example, the hand is part of the superior
extremity).

Inferior or caudal - away from the head; lower (example, the foot is part of the inferior extremity).

Anterior or ventral - front (example, the kneecap is located on the anterior side of the leg).

Posterior or dorsal - back (example, the shoulder blades are located on the posterior side of the body).

Medial - toward the midline of the body (example, the middle toe is located at the medial side of the foot).

Lateral - away from the midline of the body (example, the little toe is located at the lateral side of the foot).

Proximal - toward or nearest the trunk or the point of origin of a part (example, the proximal end of the femur
joins with the pelvic bone).

Distal - away from or farthest from the trunk or the point or origin of a part (example, the hand is located at
the distal end of the forearm).
Planes of the Body

Coronal Plane (Frontal Plane) - A vertical plane running from side to side; divides the body or any of its
parts into anterior and posterior portions.

Sagittal Plane (Lateral Plane) - A vertical plane running from front to back; divides the body or any of its
parts into right and left sides.

Axial Plane (Transverse Plane) - A horizontal plane; divides the body or any of its parts into upper and lower
parts.

Median plane - Sagittal plane through the midline of the body; divides the body or any of its parts into right
and left halves.