AJAY-9971313179

ASSIGNMENT
(Tutor Marked Assignment)
Cell Biology
Course Code: LSE- 01
Assignment Code: LSE-01/TMA/2020
Maximum Marks: 100

11.Explain the reactions of tricarboxylic acid (TCA) cycle and its role in (10)
.energy production.

Tricarboxylic acid cycle, (TCA cycle), also called Krebs cycle and citric acid
cycle, the second stage of cellular respiration, the three-stage process by which
living cells break down organic fuel molecules in the presence of oxygen to
harvest the energy they need to grow and divide. This metabolic process occurs
in most plants, animals, fungi, and many bacteria. In all organisms except
bacteria the TCA cycle is carried out in the matrix of intracellular structures
called mitochondria.
The TCA cycle plays a central role in the breakdown, or catabolism, of organic fuel
molecules—i.e., glucose and some other sugars, fatty acids, and some amino acids.
Before these rather large molecules can enter the TCA cycle they must be degraded
into a two-carbon compound called acetyl coenzyme A (acetyl CoA). Once fed into
the TCA cycle, acetyl CoA is converted into carbon dioxide and energy.
The TCA cycle consists of eight steps catalyzed by eight different enzymes
(see Figure). The cycle is initiated (1) when acetyl CoA reacts with the compound
oxaloacetate to form citrate and to release coenzyme A (CoA-SH). Then, in a
succession of reactions, (2) citrate is rearranged to form isocitrate; (3) isocitrate
loses a molecule of carbon dioxide and then undergoes oxidation to form alpha-
ketoglutarate; (4) alpha-ketoglutarate loses a molecule of carbon dioxide and is
oxidized to form succinyl CoA; (5) succinyl CoA is enzymatically converted to
succinate; (6) succinate is oxidized to fumarate; (7) fumarate is hydrated to produce
malate; and, to end the cycle, (8) malate is oxidized to oxaloacetate. Each complete
turn of the cycle results in the regeneration of oxaloacetate and the formation of two
molecules of carbon dioxide.

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Energy is produced in a number of steps in this cycle of reactions. In step 5, one

molecule of adenosine triphosphate (ATP), the molecule that powers most
cellular functions, is produced. Most of the energy obtained from the TCA
cycle, however, is captured by the compounds nicotinamide adenine
dinucleotide (NAD+) and flavin adenine dinucleotide (FAD) and converted later
to ATP. Energy transfers occur through the relay of electrons from one
substance to another, a process carried out through the chemical reactions
known as oxidation and reduction, or redox reactions. (Oxidation involves the
loss of electrons from a substance and reduction the addition of electrons.) For
each turn of the TCA cycle, three molecules of NAD+ are reduced to NADH and
one molecule of FAD is reduced to FADH2. These molecules then transfer their
energy to the electron transport chain, a pathway that is part of the third stage of
cellular respiration. The electron transport chain in turn releases energy so that it
can be converted to ATP through the process of oxidative phosphorylation.

2.
2(a) Describe the structure and function of nuclear envelope. (5)
.
The nuclear envelope, also known as the nuclear membrane, is made up of (5)
two lipid bilayer membranes which in eukaryotic cells surrounds the nucleus, which
encases the genetic material.
The nuclear envelope consists of two lipid bilayer membranes, an inner nuclear
membrane, and an outer nuclear membrane. The space between the membranes is
called the perinuclear space. It is usually about 20–40 nm wide. The outer nuclear
membrane is continuous with the endoplasmic reticulum membrane. The nuclear
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envelope has many nuclear pores that allow materials to move between
the cytosol and the nucleus. Intermediate filaments form a lamina internally to the
inner nuclear membrane, and more loosely externally to the outer nuclear
membrane to give structural support to the nucleus.
The nuclear envelope is made up of two lipid bilayer membranes. An inner nuclear
membrane and an outer nuclear membrane. These membranes are connected to each
other by nuclear pores. Two sets of intermediate filaments provide support for the
nuclear envelope. An internal network forms the nuclear lamina on the inner
nuclear membrane. A looser network forms outside to give external support.
Outer membrane
The outer nuclear membrane also shares a common border with the endoplasmic
reticulum. While it is physically linked, the outer nuclear membrane contains
proteins found in far higher concentrations than the endoplasmic reticulum. All
four nesprin proteins (nuclear envelope spectrin repeat proteins) present in
mammals are expressed in the outer nuclear membrane. Nesprin proteins connect
cytoskeletal filaments to the nucleoskeleton. Nesprin-mediated connections to the
cytoskeleton contribute to nuclear positioning and to the cell’s mechanosensory
function. KASH domain proteins of Nesprin-1 and -2 are part of a LINC
complex (linker of nucleoskeleton and cytoskeleton) and can bind directly to
cystoskeletal components, such as actin filaments, or can bind to proteins in the
perinuclear space. Nesprin-3 and-4 may play a role in unloading enormous cargo;
Nesprin-3 proteins bind plectin and link the nuclear envelope to cytoplasmic
intermediate filaments. Nesprin-4 proteins bind the plus end directed motor kinesin-
1. The outer nuclear membrane is also involved in development, as it fuses with the
inner nuclear membrane to form nuclear pores.
Inner membrane
The inner nuclear membrane encloses the nucleoplasm, and is covered by
the nuclear lamina, a mesh of intermediate filaments which stabilizes the nuclear
membrane as well as being involved in chromatin function and entire expression. It
is connected to the outer membrane by nuclear pores which penetrate the
membranes. While the two membranes and the endoplasmic reticulum are linked,
proteins embedded in the membranes tend to stay put rather than dispersing across
the continuum. It is lined with a fiber network called the nuclear lamina which is
10-40 nm thick and provides strength.
Mutations in the inner nuclear membrane proteins can cause several nuclear
envelopathies.
Nuclear pores

Nuclear pores crossing the nuclear envelope

The nuclear envelope is punctured by thousands of nuclear pores, large
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hollow protein complexes about 100 nm across, with an inner channel about 40 nm
wide. They link the inner and outer nuclear membranes.

(b) Explain the molecular theory of recombination.

Genetic recombination (also known as genetic reshuffling) is the exchange of
genetic material between different organisms which leads to production of offspring
with combinations of traits that differ from those found in either parent.
In eukaryotes, genetic recombination during meiosis can lead to a novel set
of genetic information that can be passed on from the parents to the offspring. Most
recombination is naturally occurring.
During meiosis in eukaryotes, genetic recombination involves the pairing
of homologous chromosomes. This may be followed by information transfer
between the chromosomes. The information transfer may occur without physical
exchange (a section of genetic material is copied from one chromosome to another,
without the donating chromosome being changed) (see SDSA pathway in Figure);
or by the breaking and rejoining of DNA strands, which forms new molecules of
DNA (see DHJ pathway in Figure).
Recombination may also occur during mitosis in eukaryotes where it ordinarily
involves the two sister chromosomes formed after chromosomal replication. In this
case, new combinations of alleles are not produced since the sister chromosomes
are usually identical. In meiosis and mitosis, recombination occurs between similar
molecules of DNA (homologous sequences). In meiosis, non-sister homologous
chromosomes pair with each other so that recombination characteristically occurs
between non-sister homologues. In both meiotic and mitotic cells, recombination
between homologous chromosomes is a common mechanism used in DNA repair.
Gene conversion - the process during which homologous sequences are made
identical also falls under genetic recombination.
Genetic recombination and recombinational DNA repair also occurs
in bacteria and archaea, which use asexual reproduction.
Recombination can be artificially induced in laboratory (in vitro) settings,
producing recombinant DNA for purposes including vaccine development.
V(D)J recombination in organisms with an adaptive immune system is a type of
site-specific genetic recombination that helps immune cells rapidly diversify to
recognize and adapt to new pathogens.

3
3(a) Describe the components of fluid connective tissue in animals. (7)
.Fluid connetive tissue is blood.Its components are RBCs,WBCs,platelets (3)
Plasma: It is the liquid part of blood. It is straw coloured. It contains (91-92) %
water and (8-9) % organic and inorganic materials. The organic substances include
various types of blood protein and waste materials. The inorganic part contains
different minerals like sodium, potassium, iron. calcium, magnesium etc.Blood
Cell or Blood Corpuscles: Blood corpuscles form the major components of blood.
Blood cells are of three types. These are:

Red Blood Corpuscle or Erythrocyte: These blood corpuscles contain

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haemoglobin. Due to haemoglobin colour of blood is red. the red blood corpuscles
of the amphibians are biconvex, nucleated and oval. On the contrary, the red
corpuscles of the blood of mammals are biconvex, non nucleated and round.
Haemoglobin is combined with oxygen forms a unstable compound
oxyhaemoglobin. It breaks down and releases oxygen in places where it is needed.

Functions: To, carry oxygen and some carbon dioxide.

White Blood Corpuscle or Leucocyte:These generally lack definite shape and are
nucleated. Cytoplasm of white corpuscles are either granular or non granular.

Functions: To destroy germs and take part in self defense.

Thrombocyte or Platelets: These are present in the blood of vertebrate animals.

These are usually nucleated and spindle shaped. Nucleus is absent in the
Thrombocytes of mammals. The thrombocyte of mammal is also called platelet.

Function: Thrombocytes take part in blood coagulation or blood clotting.

(b) What is meristem? Discuss its role in plants.

A meristem is the tissue in most plants containing undifferentiated cells
(meristematic cells), found in zones of the plant where growth can take place.
Meristematic cells give rise to various organs of a plant and are responsible for
growth.
Differentiated plant cells generally cannot divide or produce cells of a different
type. Meristematic cells are incompletely or not at all differentiated, and are capable
of continued cellular division. Therefore, cell division in the meristem is required to
provide new cells for expansion and differentiation of tissues and initiation of new
organs, providing the basic structure of the plant body. Furthermore, the cells are
small and protoplasm fills the cell completely. The vacuoles are extremely small.
The cytoplasm does not contain
differentiated plastids (chloroplasts or chromoplasts), although they are present in
rudimentary form (proplastids). Meristematic cells are packed closely together
without intercellular cavities. The cell wall is a very thin primary cell wall as well
as some are thick in some plants. Maintenance of the cells requires a balance
between two antagonistic processes: organ initiation and stem cell population
renewal.
There are three types of meristematic tissues: apical (at the tips), intercalary (in the
middle) and lateral (at the sides). At the meristem summit, there is a small group of
slowly dividing cells, which is commonly called the central zone. Cells of this zone
have a stem cell function and are essential for meristem maintenance. The
proliferation and growth rates at the meristem summit usually differ considerably
from those at the periphery.
The term meristem was first used in 1858 by Carl Wilhelm von Nägeli (1817–1891)
in his book Beiträge zur Wissenschaftlichen Botanik ("Contributions to Scientific
Botany"). It is derived from the Greek word merizein (μερίζειν), meaning to divide,
in recognition of its inherent function.

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Meristem tissue and plant development

Meristematic tissues are cells or group of cells that have the ability to divide. These
tissues in a plant consist of small, densely packed cells that can keep dividing to
form new cells. Meristematic tissue is characterized by small cells, thin cell walls,
large cell nuclei, absent or small vacuoles, and no intercellular spaces.

Meristematic tissues are found in many locations, including near the tips of roots
and stems (apical meristems), in the buds and nodes of stems, in the cambium
between the xylem and phloem in dicotyledonous trees and shrubs, under the
epidermis of dicotyledonous trees and shrubs (cork cambium), and in the pericycle
of roots, producing branch roots. The two types of meristems are primary meristems
and secondary meristems.

Meristem Zones

The apical meristem, also known as the “growing tip,” is an undifferentiated

meristematic tissue found in the buds and growing tips of roots in plants. Its main
function is to trigger the growth of new cells in young seedlings at the tips of roots
and shoots and forming buds. Apical meristems are organized into four zones: (1)
the central zone, (2) the peripheral zone, (3) the medullary meristem and (3) the
medullary tissue.

Meristematic zones: Each zone of the apical meristem has a particular function.
Pictured here are the (1) central zone, (2) peripheral zone, (3) medullary meristem
and (3) medullary tissue.

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Apical meristem: The apical meristem, pictured in the center of the leaves of this
image, is also termed the “growing tip”. Its main function is to begin growth of new
cells in young seedlings at the tips of roots and shoots (forming buds, among other
things).

The central zone is located at the meristem summit, where a small group of slowly
dividing cells can be found. Cells of this zone have a stem cell function and are
essential for meristem maintenance. The proliferation and growth rates at the
meristem summit usually differ considerably from those at the periphery.
Surrounding the central zone is the peripheral zone. The rate of cell division in the
peripheral zone is higher than that of the central zone. Peripheral zone cells give
rise to cells which contribute to the organs of the plant, including leaves,
inflorescence meristems, and floral meristems.

An active apical meristem lays down a growing root or shoot behind itself, pushing
itself forward. They are very small compared to the cylinder-shaped lateral
meristems, and are composed of several layers, which varies according to plant
type. The outermost layer is called the tunica, while the innermost layers are
cumulatively called the corpus.

4.
4Differentiate between the following pairs: (10)
.(a) Procaryotes and Eucaryotes

The distinction between prokaryotes and eukaryotes is considered to be the

most important distinction among groups of organisms. Eukaryotic cells contain
membrane-bound organelles, such as the nucleus, while prokaryotic cells do
not. Differences in cellular structure of prokaryotes and eukaryotes include the
presence of mitochondria and chloroplasts, the cell wall, and the structure
of chromosomal DNA.
Prokaryotes were the only form of life on Earth for millions of years until more
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complicated eukaryotic cells came into being through the process of evolution.
Differences Between Eukaryotic and Prokaryotic Cells
The difference between the structure of prokaryotes and eukaryotes is so great
that it is considered to be the most important distinction among groups of
organisms.

 The most fundamental difference is that eukaryotes do have "true" nuclei

containing their DNA, whereas the genetic material in prokaryotes is not
membrane-bound.

Structure and contents of a typical Gram-positive bacterium cell (a prokaryotic

cell)

 In eukaryotes, the mitochondria and chloroplasts perform various metabolic

processes and are believed to have been derived from endosymbiotic bacteria.
In prokaryotes similar processes occur across the cell membrane;
endosymbionts are extremely rare.

 The cell walls of prokaryotes are generally formed of a different molecule

(peptidoglycan) to those of eukaryotes (many eukaryotes do not have a cell wall
at all).

 Prokaryotes are usually much smaller than eukaryotic cells.

 Prokaryotes also differ from eukaryotes in that they contain only a single loop
of stable chromosomal DNA stored in an area named the nucleoid, while
eukaryote DNA is found on tightly bound and organised chromosomes.
Although some eukaryotes have satellite DNA structures called plasmids, these
are generally regarded as a prokaryote feature and many important genes in
prokaryotes are stored on plasmids.

 Prokaryotes have a larger surface area to volume ratio giving them a higher
metabolic rate, a higher growth rate and consequently a shorter generation time
compared to Eukaryotes.

 Genes
o Prokaryotes also differ from eukaryotes in the structure, packing, density, and
arrangement of their genes on the chromosome. Prokaryotes have incredibly
compact genomes compared to eukaryotes, mostly because prokaryote genes
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lack introns and large non-coding regions between each gene.

o Whereas nearly 95% of the human genome does not code for proteins
or RNA or includes a gene promoter, nearly all of the prokaryote genome
codes or controls something.
o Prokaryote genes are also expressed in groups, known as operons, instead of
individually, as in eukaryotes.
o In a prokaryote cell, all genes in an operon(three in the case of the famous lac
operon) are transcribed on the same piece of RNA and then made into
separate proteins, whereas if these genes were native to eukaryotes, they each
would have their own promoter and be transcribed on their own strand of
mRNA. This lesser degree of control over gene expression contributes to the
simplicity of the prokaryotes as compared to the eukaryotes.

(b) Mitochondria and Chloroplast

Following are the key difference between the two most important organelles of the
cell:

1. Mitochondria are the large, membrane-bound, bean-shaped organelle found

in almost all kind of eukaryotic organism, also known as ‘powerhouse of the
cell’. Mitochondria are responsible for cellular respiration and energy
metabolism. Conversely, Chloroplast is found only in green plants and in few
algae, they are the sites of photosynthesis. This organelle of the cell is much
more complex and larger than the mitochondria.
2. Mitochondria are present in the cells of all types of aerobic organisms like
plants and animals, whereas Chloroplast is present in green plants and some
algae, protists like Euglena. Mitochondria is the colourless, bean
shape organelles. Chloroplasts are green colour and disc shape organelles.
3. Mitochondria and Chloroplast have two chambers inside them which is
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the matrix and the cristae in mitochondria, stroma, and thylakoids in a

chloroplast.
4. The inner membrane of mitochondria is folded into cristae while that of a
chloroplast, rises into flattened sacs called as thylakoids.
5. The thylakoid membrane in chloroplast contains carotenoids, chlorophyll, and
photosynthetic pigments, but these are absent in mitochondria. Mitochondria
convert sugar (glucose) into chemical energy called as ATP (adenosine
triphosphate), it uses oxygen and release energy by breaking the organic food
and in turn produces carbon dioxide along with water. In chloroplast the solar
energy is stored, this organelle helps in storing the energy, further it also uses
carbon dioxide and water to make glucose. Chloroplast liberates or releases
oxygen.
6. Mitochondria are the site for beta oxidative, photorespiration, oxidative
phosphorylation, ETC; Chloroplast is the site for the photorespiration and
photosynthesis.

(c) Animal and Plant cells

Below are the important points which differentiate the plant cells and animal cells
regarding their features:

1. The fundamental and functional unit of life – The Cell, which can be
prokaryotic or eukaryotic, single celled or multi-celled. But eukaryotes are
further divided as Kingdom Plantae and Kingdom Animalia.These are the
types of multicellular, Eukaryotic cells, having many features common but
plant cell possess certain other organelles such as the cell wall, chloroplast,
and the vacuoles. These organelles are found to be absent in animal cells.
2. The Plant Cells are usually larger, which has fixed and rectangular shape,
while animal cells are comparatively smaller in size, irregular and round.
3. The most important feature of Plant Cell is the presence of cell wall, along
with the plasma membrane, while Animal cells do not possess
cell wall, but plasma membrane is present.
4. The nucleus is present in both the cells, but in Plant cell it lies on one side
while it is present in the center of the Animal cell.
5. Centrosomes/Centrioles, Cilia, Desmosomes, Lysosomes are the organelles
found absent in Plant cells, while they exist in Animal Cells.
6. Plastids, Glyoxysomes, Plasmodesmata, Chloroplast (for the preparation of
food) are the features present in the Plant Cells but not found in Animal
cells.
7. There is a huge vacuole present in Plant cells, but numerous and small
vacuoles are present in Animal Cells.
8. Mitochondria if present is fewer in number, though they play a significant role
in Animal Cells and are present in numbers. In Animal Cells they help in the
production of energy.
9. The storing of energy is done by Chloroplast in Plant cells, which is absent

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in Animal Cells.
10. The reserve food material is Starch in Plant Cell and Glycogen in Animal
Cells.
11. Synthesis of nutrients like amino acids, vitamins, and coenzymes is performed
by the Plant cells, but Animal Cells are unable to do so.
12. Cytokinesis occurs by cell plate only in Plant Cells whereas in Animal Cells it
occurs by furrowing or constrictions.

(d) Fluorescence microscopy and Phase contrast microscopy

Phase-contrast microscopy is an optical microscopy technique that converts phase
shifts in light passing through a transparent specimen to brightness changes in the
image. Phase shifts themselves are invisible, but become visible when shown as
brightness variations.
When light waves travel through a medium other than vacuum, interaction with the
medium causes the wave amplitude and phase to change in a manner dependent on
properties of the medium. Changes in amplitude (brightness) arise from the
scattering and absorption of light, which is often wavelength-dependent and may
give rise to colors. Photographic equipment and the human eye are only sensitive to
amplitude variations. Without special arrangements, phase changes are therefore
invisible. Yet, phase changes often carry important information.
Phase-contrast microscopy is particularly important in biology. It reveals
many cellular structures that are not visible with a simpler bright-field microscope,
as exemplified in the figure. These structures were made visible to earlier
microscopists by staining, but this required additional preparation and thus killing
the cells. The phase-contrast microscope made it possible for biologists to study
living cells and how they proliferate through cell division. It is one of the few
methods available to quantify cellular structure and components that does not
use fluorescence. After its invention in the early 1930s, phase-contrast microscopy
proved to be such an advancement in microscopy that its inventor Frits Zernike was
awarded the Nobel Prize in Physics in 1953.

55.Explain the characteristics of enzyme and mechanism of its action. (5+5)

An
. enzyme attracts substrates to its active site, catalyzes the chemical reaction by
which products are formed, and then allows the products to dissociate (separate
from the enzyme surface). The combination formed by an enzyme and its substrates
is called the enzyme–substrate complex. When two substrates and one enzyme are
involved, the complex is called a ternary complex; one substrate and one enzyme
are called a binary complex. The substrates are attracted to the active site by
electrostatic and hydrophobic forces, which are called noncovalent bonds because
they are physical attractions and not chemical bonds. As an example, assume two
substrates (S1 and S2) bind to the active site of the enzyme during step 1 and react to
form products (P1 and P2) during step 2. The products dissociate from the enzyme
surface in step 3, releasing the enzyme. The enzyme, unchanged by the reaction, is
able to react with additional substrate molecules in this manner many times per
second to form products. The step in which the actual chemical transformation
occurs is of great interest, and, although much is known about it, it is not yet fully
understood. In general there are two types of enzymatic mechanisms, one in which
a so-called covalent intermediate forms and one in which none forms.
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In the mechanism by which a covalent intermediate—i.e., an intermediate with a

chemical bond between substrate and enzyme—forms, one substrate, B―X, for
example, reacts with the group N on the enzyme surface to form an enzyme-
B intermediate compound. The intermediate compound then reacts with the second
substrate, Y, to form the products B―Y and X.
Many enzymes catalyze reactions by this type of
mechanism. Acetylcholinesterase is used as a specific example in the sequence
described below. The two substrates (S1 and S2) for acetylcholinesterase are
acetylcholine (i.e., B―X) and water (Y). After acetylcholine (B―X) binds to the
enzyme surface, a chemical bond forms between the acetyl moiety (B) of
acetylcholine and the group N (part of the amino acid serine) on the enzyme
surface. The result of the formation of this bond, called an acyl–serine bond, is one
product, choline (X), and the enzyme-B intermediate compound (an acetyl–enzyme
complex). The water molecule (Y) then reacts with the acyl–serine bond to form the
second product, acetic acid (B―Y), which dissociates from the enzyme.
Acetylcholinesterase is regenerated and is again able to react with another molecule
of acetylcholine. This kind of reaction, involving the formation of an intermediate
compound on the enzyme surface, is generally called a double displacement
reaction.
Sucrose phosphorylase acts in a similar way. The substrate for sucrose
phosphorylase is sucrose, or glucosyl-fructose (B―X), and the group N on the
enzyme surface is a chemical group called a carboxyl group (COOH). The enzyme-
B intermediate, a glucosyl–carboxyl compound, reacts with phosphate (Y) to form
glucosyl-phosphate (B―Y). The other product (X) is fructose.
In double displacement reactions, the covalent intermediate between enzyme and
substrate apparently influences the reaction to proceed more rapidly. Because the
enzyme is unaltered at the end of the reaction, it functions as a true catalyst, even
though it is temporarily altered during the enzymatic process.
Although many enzymes form a covalent intermediate, the mechanism is not
essential for catalysis. One substrate (Y) reacts directly with the second substrate
(X―B), in a so-called single displacement reaction. The B moiety, which is
transformed in the chemical reaction, is involved in only one reaction and does not
form a bond with a group on the enzyme surface. The enzyme maltose
phosphorylase, for example, directly affects the bonds of the substrates
(B―X and X), which, in this case, are maltose (glucosylglucose) and phosphate, to
form the products, glucose (X) and glucosylphosphate (B―Y).
Covalent intermediates between part of a substrate and an enzyme occur in many
enzymatic reactions, and various amino acids—serine, cysteine, lysine, and
glutamic acid—are involved.

6 (20)
.
6.Describe the steps involved in protein synthesis in prokaryotes.
Protein synthesis in the cell is conducted by ribosomes that are found attached to
the membrane of endoplasmic reticulum and microsomes, as well as in free state in
the groundplasm.

The main components that take part in protein synthesis at cellular level are: 20
different amino acids, different types of RNAs, enzymes, aminoacid activating
enzymes, polypeotide-polymerase and energy liberating molecules, such as ATP
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and GTP.

DNA which contains genetic information synthesizes three kinds of RNA:

(i) Messenger RNA (mRNA)

(ii) Ribosomal RNA (rRNA) and

(iii) Transfer RNA (tRNA) or soluble RNA (sRNA).

mRNA is copied from DNA molecule. The specific locus of DNA molecule where
mRNA is formed is referred to as a structural gene. tRNAs come probably from
special genes called determinants for tRNAs.

A Protein Synthesis in Prokaryotes:

The mechanism of protein synthesis has been thoroughly investigated in
Escherichia coli. In bacterial cell, the protein synthesis takes place on 70s
ribosomes.

The process of protein synthesis in E. coli involves the following steps:

1. Transcription:
The partial uncoiling of two DNA strands occurs. This is followed by the
production of single stranded mRNA on one of the two DNA strands. The
messenger RNA complement is made in accordance with base pairing rules. This is
transcription.

The transcription of genetic code of DNA into mRNA is catalysed by the enzyme
RNA polymerase. mRNA carries the information in the form of base triplets for the
synthesis of a particular protein (Fig. 20.2).

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2. The second step involves the separation of mRNA from DNA and then its
transfer from nucleus to cytoplasm and final attachment of 5′ end of mRNA with
30s (smaller) sub-unit of ribosome in presence of protein initiation factor. Before
the mRNA migrates from nucleus to ribosome in cytoplasm it undergoes process of
maturation.

In eukaryotes the newly formed RNA is called heterogenous nuclear RNA (hn
RNA). Many of the functional RNA molecules including ?RNA and mRNA in
eukaryotes are processed from much longer precursor RNAs which are 5,000 to
50,000 nucleotides long and may be 10 to 100 times longer than the mature
functional RNA molecules which are derived from them.

Precursor RNAs are transcripts of split genes which contain both sequences coding
for aminoacids (exons) and those not coding for aminoacids (introns) interspersed.
The non-coding sequences from the pre-RNAs are cleaved out and coding
sequences are spliced together to produce functional mature RNA molecules.

Few of the eukaryotic genes are not split. In prokaryotes some of the RNA
molecules are cleavage products of longer pre-RNA.

3. Translation:
As has been pointed out, mRNA determines the sequence of amino acids in the
polypeptide chain which in turn is determined by sequence of nucleotides in DNA
(gene). This process is called translation. Translation involves the following steps
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which are shown in Figs. 20.2, 20.3, 20.4.

(a) Activation of aminoacid:

Elsewhere in the cytoplasm, aminoacids are selected for activation. Professor Fritz
Libmann and others discovered in 1956 that before amino acids can combine to
form proteins, they must be activated and this is achieved by combining with
phosphate. The activation involves the reaction between aminoacid and ATP.

The reaction is catalysed by specific enzyme aminoacyl RNA synthesize. So, for
the activation of 20 aminoacids there should be at least a set of 20 such enzymes in
the cytoplasm. Amino acid activating enzymes were first discovered by M.
Hoagland.

The product formed after activation is aminoacyl-adenylate enzyme complex which

is energy rich compound.

(b) Attachment of activated aminoacid to tRNA:

The CCA end of tRNA molecule now attaches with specific aminoacid adenylate-
enzyme complex. The aminoacyl-adenylate remains attached to the enzyme in the
form of monocovalent complex until it is transferred to tRNA. The carboxyl group
of aminoacid residue of aminoacyl adenylate is transferred to 3′ OH group of ribose
sugar of terminal adenosine at CCA end of tRNA. As a result, aminoacyl-tRNA,
AMP and enzyme are formed.

The transfer of aminoacids to tRNA is catalysed by the previous aminoacyl RNA

synthetase enzyme itself (Fig. 20.3).

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(c) The aminoacids – tRNA complex then comes to mRNA where adapter
nucleotide triplet or anticodon of tRNA becomes attached with the complementary
base triplet (codon) of mRNA.

The fate of amino acid is determined at the very moment, it becomes attached with
the corresponding tRNA. The messenger RNA and tRNA-amino acid complex
attachment is temporary. Like this, many /RN A-amino acid complexes are
arranged one after another at proper places on messenger RNA strand in linear
fashion. In the attachment, the adapter trinuceleotides of rRNAs act as anticodons
(Figs. 20.4 and 20.5).

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The mRNA molecules have translation initiation site at 5′ end and the chain
termination site close to trailor end. The initiation site consists of a codon AUG and
unknown secondary structure of mRNA. The chain termination site has one of the
three codons UAA, UAG and UGA.

Mature mRNA binds with smaller ribosomal sub-unit in presence of initiation factor
IF2. Soon tRNA-N-Formyl methionine complex (F met-tRNA) comes from the
cytoplasmic amino acid pool and binds with the first triplet codon of mRNA to
initiate the process of protein synthesis and to form initiation complex.
Initiation complex is formed in presence of guanosine triphosphate (GTP) and three
protein factors F1, F2 and F3. This is followed by union of bigger sub-unit with
smaller ribosomal sub-unit in presence of Mg++ and initiation factors F1, F2 to form
the ribosome. The codes of mRNA are not read by a single ribosome but by many
ribosomes interlinked by mRNA (Polysomes).
(d) Initiation of Protein Synthesis:
The messenger RNA always has first triplet as AUG or GUG at its 5-end and these
triplets code for aminoacids N-formyl methionine (F. met) which usually initiates a
protein chain.

Thus, in all proteins formyl methionine occupies the first place, i.e., at, amino end
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and when the protein molecules are completely synthesised formyl methionine may
be detached from the protein molecules by activity of hydrolytic enzyme
deformylase.

In formyl methionine- tRNA complex the amino group is blocked by formyl group
leaving only COOH group free to react with NH2 group of the second amino acid
(AA2). In this way, polypeptide chain always grows from amino end toward-COOH
end.
When one tRNA-aminoacid complex attaches to mRNA at starting end, then the
second tRNA-aminoacid complex also comes just after the first and finally the two
adjacent amino acids form peptide linkage. Like this several molecules of amino
acids will join in a definite order through peptide bonds to form specific protein
molecule (Fig. 20.5).

(e) Elongation of Polypeptide Chain:

The peptide chain elongates by regular addition of aminoacids and relative
movement of ribosome along with messenger RNA in presence of GTP
(guanosine triphosphate) in the following sequence:
(a) According to W.D. Stansfield (1969) there are three presumed sites in the
ribosome Figs. 20.3 and 20.4. These are:
(i) Decoding site or ‘A’ site which binds the loaded AA~tRNA complex with the
mRNA by base pairing.

(ii) A condensing site or ‘P’ site or peptidyl site which joins the aminoacid to the
growing polypeptide chain.

(iii) An exit site or ‘E’ site at which tRNA detaches from the polypeptide,
messenger RNA and ribosome.

tRNA with their associated aminoacids will enter the ribosomal site ‘A’ and will be
checked by a ‘checking factor’ to see if there is a correct fit between the codon on
the messengers RNA and the anticodon of tRNA. If the fit is incorrect, the tRNA is

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rejected and presumably other /RNAs will continue to be tried until the correct one
is found.

(b) As the initiating codon AUG or GUG has entered the ribosome and is in
position facing the site ‘A’, the correct tRNA, i.e., f-met-tRNA is checked against
codon. This reaction is facilitated by the presence of initiation factor F1

(c) The 30S f-met-tRNA along with messenger RNA, then moves from decoding
site (‘A’ site) to peptidyl site (‘P’ site) and with this the next codon of mRNA enters
‘A’ site where it finds the second correct aminoacyl-tRNA. Aminoacyl-tRNA
(AA2 – tRNA) binds with the codon of ‘A’ site in presence of GTP and two proteins
called transfer factor Tu and Ts which remain associated with ribosomes.
In this binding process, a complex is formed from GTP, the transfer factors and the
incoming aminoacyl-tRNA which ultimately fixes aminoacyl-tRNA (AA2 tRNA) at
the ‘A’ site of ribosome and at the same time releases transfer factors – GTP
complex and inorganic phosphate.
(d) Due to the relative movement of ribosome and mRNA in presence of single
GTP molecule the next codon enters the ‘A’ site. The A site is now occupied by
another aminoacyl- tRNA (AA3– tRNA) corresponding to the next codon of mRNA
and f-met-tRNA reaches at the exit site (E-site) and AA2-tRNA occurs at the P site.
Now an enzyme known as transferase I kicks off tRNA from formyl methionine and
flips the formyl methione (AA1,) to AA2-tRNA bound at the ‘P’ site.
According to Monro (1967) an enzyme known as peptidyl synthetase found in SOS,
sub-unit helps in the formation of peptide bond. The ‘G’ factor is supposed to
release the discharged or deacetylated tRNA from the site ‘E’ of ribosome.

(e) The next stage of elongation process follows that involves establishment of
peptide bond by reaction between free NH2 group of incoming amino acid and
carboxyl group of the polypeptide.
Thus, during the elongation of polypeptide chain, each charged tRNA (aminoacyl-
tRNA) enters the decoding site, moves to ‘P’ site, transfers its aminoacid to the
carboxyl end of polypeptide, moves to exit site where polypeptide chain is
transferred to adjacent tRNA bound at ‘P’ site and then finally released from the
ribosome.

The synthesis of polypeptide chain is completed according to the codons of

messenger RNA and the process comes to an end abruptly where any one of the
three non-sense triplets UAG, UAA and UGA is present in the messenger RNA.
Generally, no tRNA has anticodon for any of these three ‘nonsense codons’ but

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some suppressor mutations produce tRNA with any of these three codons.

7 (3+7)
.7.What is cell cycle? Explain how cell cycle times are determined.
The
8 cell cycle is the process a cell will go through to replicate all of its material and (20)
divide
. itself from one cell into two identical cells. While this is commonly known
as Mitosis, in fact Mitosis is just one stage of the cell cycle. In this article, we will
look at the different stages of the cell cycle and what happens in each stage. We will
also consider the regulation of the cell cycle, and look at some examples of when
this goes wrong.
Phases of the Cell Cycle
The Cell Cycle is a 4-stage process consisting of Gap 1 (G1), Synthesis, Gap 2 (G2)
and Mitosis. An active eukaryotic cell will undergo these steps as it grows and
divides. After completing the cycle, the cell either starts the process again from G1
or exits the cycle through G0. From G0, the cell can undergo terminal
differentiation.

G1 phase

 Cell increases in size

 Cellular contents duplicated

S phase

 DNA replication
 Each of the 46 chromosomes (23 pairs) is replicated by the cell

G2 phase

 Cell prepares for cell division

M phase

 Mitosis followed by Cytokinesis (cell separation)

 Formation of two identical daughter cells

By Simon Caulton (Own work) [CC BY-SA 3.0

(http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

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Fig 1.0 – Diagram showing the stages of the cell cycle.

Phases of Mitosis
The M phase involves Mitosis which is the process of cell division. It is composed
of:

Prophase

 Nucleolus disintegrates
 Nuclear membrane breakdown
 Spindle fibres appear

Prometaphase

 Spindle fibres attach to chromosomes

 Chromosomes condense

Metaphase

 Chromosomes align at the metaphase plate

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Anaphase

 Centromeres divide
 Sister chromatids move to opposite poles

Telophase

 Nuclear membrane reforms

 Chromosomes decondense
 Spindle fibres disappear

Cytokinesis is the process of the parent cell becoming 2 daughter cells. These
daughter cells contain identical genetic information. Cytokinesis also involves a
division of the cytoplasm. It is considered a separate step to mitosis.

The stages in the cell cycle between one mitosis and the next, which includes G1, S
and G2, is known as interphase.

Further details on the process of mitosis can be found here.

Regulation
The progression of cells through the cell cycle is controlled by checkpoints at
different stages. These detect if a cell contains damaged DNA and ensure those
cells do not replicate. The Restriction point (R) is located at G1 and is a key
checkpoint. The vast majority of cells that pass through the R point will end up
completing the entire cell cycle. Other checkpoints are located at the transitions
between G1 and S, and G2 and M.

If damaged DNA is detected at any checkpoint, activation of the checkpoint results

in increased protein p53 production. p53 is a tumour suppressor gene that stops the
progression of the cell cycle and starts repair mechanisms for the damaged DNA. If
this DNA cannot be repaired, then it ensures the cell undergoes apoptosis and can
no longer replicate.

This cell cycle is also closely regulated by cyclins which control cell progression by
activating cyclin-dependent kinase (CDK) enzymes.

An example of a tumour suppressor protein would be retinoblastoma

protein (Rb). Rb restricts the ability of a cell to progress from G1 to S phase in the
cell cycle. CDK phosphorylates Rb to pRb, making it unable to restrict cell
proliferation. This allows cells to divide normally in the cell cycle.

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8.Write short notes on the following:

(a) Type of bonds
Sometimes, bonds one of a kind sorts of atoms or ions, as in NaCl or H2O. If a
substance is made of different types of atoms or ions which might be in a few way
chemically certain together, it's far called a compound. simply as an atom is the
smallest unit of an element that has all the houses of that detail, a molecule is the
smallest unit of a compound that has all of the residences of that compound.

There are 3 styles of chemical bonds you have to be familiar with.

1.Ionic bonds

2.Covalent bonds

3.Hydrogen bonds

(b) Mesenchyme

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Mesenchyme is a type of connective tissue found mostly during embryonic

development of bilateral animals (triploblasts). It is composed mainly of ground
substance with few cells or fibers. It can also refer to a group of mucoproteins
resembling mucus found, for example, in certain types of cysts. It is most easily
found as a component of Wharton's jelly.
The vitreous body of the eye is of a similar tissue.
In invertebrate zoology, the term refers to free cells loosely arranged in a matrix.
"Mesenchyme" is a term introduced by Oscar Hertwig in 1881.
In order to differentiate the use of the word mesenchyme in invertebrate zoology
(an ecto- or entomesodermal middle layer of some invertebrates) and the use in
vertebrate embryology (that is, undifferentiated tissue found in embryonic true
mesoderm - entomesoderm - from which all connective tissues like blood vessels,
blood cells, the lymphatic system, and the heart are derived.), some authors prefer
to use the term mesoglea (in wider sense) in lieu of mesenchyme when referring to
the middle layers of sponges and diploblasts, reserving the term mesenchyme for
the embryological sense. However, Brusca & Brusca discourage this usage, using
mesoglea in its strict sense (noncellular mesenchyme), and preferring to maintain
both the embryological and zoological senses for the term mesenchyme.
Finally, some similar terms used in botany generally are differentiated by the suffix
"a": mesenchyma (a tissue between xylem and phloem in
roots), collenchyma (primordial leaf tissues) and parenchyma (supportive tissues).

(c) Proton pump in photosynthesis

A proton pump is an integral membrane protein pump that builds up a proton
gradient across a biological membrane. Proton pumps catalyze the following
reaction:
H+
[on one side of a biological membrane] + energy ⇌ H+
[on the other side of the membrane]

Mechanisms are based on energy-induced conformational changes of the

protein structure or on the Q cycle.
During evolution, proton pumps have arisen independently on multiple
occasions. Thus, not only throughout nature but also within single cells,
different proton pumps that are evolutionarily unrelated can be found. Proton
pumps are divided into different major classes of pumps that utilize different
sources of energy, have different polypeptide compositions and evolutionary
origins.
Transport of the positively charged proton is typically electrogenic, i.e. it generates
an electrical field across the membrane also called the membrane potential. Proton
transport becomes electrogenic if not neutralized electrically by transport of either a
corresponding negative charge in the same direction or a corresponding positive
charge in the opposite direction. An example of a proton pump that is not
electrogenic, is the proton/potassium pump of the gastric mucosa which catalyzes a
balanced exchange of protons and potassium ions.
The combined transmembrane gradient of protons and charges created by proton
pumps is called an electrochemical gradient. An electrochemical gradient represents
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a store of energy (potential energy) that can be used to drive a multitude of

biological processes such as ATP synthesis, nutrient uptake and action potential
formation.
In cell respiration, the proton pump uses energy to transport protons from
the matrix of the mitochondrion to the inter-membrane space. It is an active pump
that generates a proton concentration gradient across the inner mitochondrial
membrane because there are more protons outside the matrix than inside. The
difference in pH and electric charge (ignoring differences in buffer capacity) creates
an electrochemical potential difference that works similar to that of a battery or
energy storing unit for the cell. The process could also be seen as analogous to
cycling uphill or charging a battery for later use, as it produces potential energy.
The proton pump does not create energy, but forms a gradient that stores energy for
later use.

(d) Cyclic AMP as second messenger

The action of epinephrine illustrates the principles by which cyclic AMP mediates hormone
action. Epinephrine is the “flight or fight hormone” that the adrenal glands release in response to
stress. The hormone causes an increase in blood pressure and the breakdown of glucose for
energy. This helps humans in danger to engage in physical activity to meet the challenges of a
situation. The body responds with a dry mouth, rapid heartbeat, and high blood pressure. A
biochemical chain of events leads to these responses. When epinephrine binds to cells, it stays
outside on the membrane‐bound receptor. The second messenger, cyclic AMP, is made by the
enzyme adenylate cyclase.

Adenylate cyclase is a two‐component enzyme system. It ultimately catalyzes the cyclase

reaction, but only when it is associated with the hormone‐bound receptor and a regulatory
protein called a stimulatory G‐protein (guanylate nucleotide binding protein), which activates
adenylate cyclase. The G‐protein is the intermediate between the receptor and the synthesis of
cyclic AMP.

G‐proteins exist either in an active or an inactive state, depending on the guanylate nucleotide
that is bound. In the inactive state, G‐protein binds to GDP. In the active state, GTP is bound to
the G‐protein. G‐proteins have an intrinsic GTPase activity, which converts bound GTP to
GDP. Hydrolysis of GTP by the G‐protein converts the G‐protein back to an inactive state. Thus
the cycle of the G‐protein is as follows:

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1. Hormone binds to receptor.

2. The hormone‐bound receptor binds to the G‐protein and causes GDP to be replaced by
GTP.

3. GTP‐bound G‐protein interacts with adenylate cyclase.

4. G‐protein hydrolyzes bound GTP to GDP, thereby going back to the ground state.

Different G‐proteins may either stimulate or inhibit adenylate cyclase to make more or less
cyclic AMP.

Cyclic AMP doesn't act directly on its target enzymes; for example, glycogen phosphorylase and
glycogen synthase. Instead, cyclic AMP stimulates a protein kinase cascade that ultimately leads
to a cellular response. Cyclic AMP binds to protein kinase A, which then catalyzes the transfer
of phosphate from ATP to a serine residue on a second enzyme, phosphorylase kinase, which
itself transfers a phosphate to glycogen phosphorylase. Active glycogen phosphorylase then
catalyzes the breakdown of glycogen to glucose‐1‐phosphate. This provides energy for muscle
activity.

Cells can't be “turned on” forever. Something must modulate the response. In fact, each step is
reversible. Starting from the target proteins, a protein phosphatase hydrolyzes the phosphate
from the proteins. Cyclic AMP is hydrolyzed by a phosphodiesterase.

Perhaps a key point in the modulation system is GTP hydrolysis by the G‐protein. This causes
adenylate cyclase to return to the unstimulated state.

All signaling mechanisms must have this modulation feature to allow the possibility of control.
For example, the Ras protein of mammalian cells is a membrane‐bound GTPase. Mutations that
decrease Ras's GTPase activity can contribute to uncontrolled growth (i.e., tumor formation) of
mammalian cells.

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