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Ans 1 a):

i) Cytochrome c is primarily known for its function in the mitochondria as a key participant in
the life-supporting function of ATP synthesis.
ii) DNA ligase is an enzyme that repairs irregularities or breaks in the backbone of double-
stranded DNA molecules.
iii) Osteoclasts, which are responsible for bone resorption, are rare cells with only 2-3 cells seen
per 1 mm3 of bone.
iv) Thrombocytes are a component of blood whose function is to stop bleeding by clumping
and clotting blood vessel injuries.
v) Gap junctions are a specialized intercellular connection between a multitude of animal cell-
types. They directly connect the cytoplasm of two cells, which allows various molecules, ions
and electrical impulses to directly pass through a regulated gate between cells.

Ans 1 b):

i) Blood
ii) prophase 1 and metaphase 1
iii) helicase
iv) chloroplasts
v) S Phase

Ans 2

a): Watson Crick Model

b):

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Ans 3 a): A photographic technique used to localize a radioactive substance within a solid
specimen; also known as radioautography.

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Autoradiography can be used to detect, and measure semiquantitatively, the radioactive materials
in almost any object that can be placed in contact with film or photographic emulsion in some
form. However, in biological research the object may be (1) a whole plant or animal that can be
flattened against a film; (2) the cut surface of a plant or animal, or one of its organs; (3) thin
sections of tissues or cells; (4) squashed or otherwise flattened cells; (5) surface films produced
by spreading on water the protein monolayers containing DNA or ribonucleic acid (RNA) that
are picked up on grids for electron microscopy; (6) sheets of paper or other materials on which
radioactive substances have been separated by chromatography or electrophoresis; or (7)
acrylamide gels in which DNA, RNA, or proteins have been separated by electrophoresis.

Ans 3 b): Mitochondria are organelles that have a double membrane structure. The outer
membrane defines the external shape of the mitochondrion. The inner membrane has many folds
called cristae. The volume between the inner and outer membranes is called the intermembrane
space, which is sometimes written "inter membrane space". The volume enclosed by the inner
membrane is called the "matrix" or, if written in full, the matrix of the mitochondrion.

The matrix of each mitochondrion contains the enzymes of the TCA cycle, which is also known
more fully as the tricarboxylic acid cycle - and also as the citric acid cycle, the Krebs cycle, and
the Szent-GyrgyiKrebs cycle. The matrix also contains other structures and molecules
including ribosomes, matrix granules and mitochondrial DNA.

Ans 4:

mRNA processing
The pre-mRNA molecule undergoes three main modifications. These modifications are 5'
capping, 3' polyadenylation, and RNA splicing, which occur in the cell nucleus before the RNA
is translated.

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5' Processing

Capping

Capping of the pre-mRNA involves the addition of 7-methylguanosine (m7G) to the 5' end. To
achieve this, the terminal 5' phosphate requires removal, which is done with the aid of a
phosphatase enzyme. The enzyme guanosyl transferase then catalyses the reaction, which
produces the diphosphate 5' end. The diphosphate 5' end then attacks the alpha phosphorus atom
of a GTP molecule in order to add the guanine residue in a 5'5' triphosphate link. The enzyme
(guanine-N7-)-methyltransferase ("cap MTase") transfers a methyl group from S-adenosyl
methionine to the guanine ring. This type of cap, with just the (m 7G) in position is called a cap 0
structure. The ribose of the adjacent nucleotide may also be methylated to give a cap 1.
Methylation of nucleotides downstream of the RNA molecule produce cap 2, cap 3 structures
and so on. In these cases the methyl groups are added to the 2' OH groups of the ribose sugar.
The cap protects the 5' end of the primary RNA transcript from attack by ribonucleases that have
specificity to the 3'5' phosphodiester bonds.

3' Processing

Cleavage and polyadenylation

The pre-mRNA processing at the 3' end of the RNA molecule involves cleavage of its 3' end and
then the addition of about 250 adenine residues to form a poly(A) tail. The cleavage and

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adenylation reactions occur if a polyadenylation signal sequence (5'- AAUAAA-3') is located
near the 3' end of the pre-mRNA molecule, which is followed by another sequence, which is
usually (5'-CA-3') and is the site of cleavage. A GU-rich sequence is also usually present
further downstream on the pre-mRNA molecule. After the synthesis of the sequence elements,
two multisubunit proteins called cleavage and polyadenylation specificity factor (CPSF) and
cleavage stimulation factor (CStF) are transferred from RNA Polymerase II to the RNA
molecule. The two factors bind to the sequence elements. A protein complex forms that contains
additional cleavage factors and the enzyme Polyadenylate Polymerase (PAP). This complex
cleaves the RNA between the polyadenylation sequence and the GU-rich sequence at the
cleavage site marked by the (5'-CA-3') sequences. Poly(A) polymerase then adds about 200
adenine units to the new 3' end of the RNA molecule using ATP as a precursor. As the poly(A)
tail is synthesised, it binds multiple copies of poly(A) binding protein, which protects the 3'end
from ribonuclease digestion.

Splicing

RNA splicing is the process by which introns, regions of RNA that do not code for proteins, are
removed from the pre-mRNA and the remaining exons connected to re-form a single continuous
molecule. Exons are sections of mRNA which become "expressed" or translated into a protein.
They are the coding portions of a mRNA molecule. Although most RNA splicing occurs after the
complete synthesis and end-capping of the pre-mRNA, transcripts with many exons can be
spliced co-transcriptionally. The splicing reaction is catalyzed by a large protein complex called
the spliceosome assembled from proteins and small nuclear RNA molecules that recognize splice
sites in the pre-mRNA sequence. Many pre-mRNAs, including those encoding antibodies, can be
spliced in multiple ways to produce different mature mRNAs that encode different protein
sequences. This process is known as alternative splicing, and allows production of a large variety
of proteins from a limited amount of DNA.

Histone mRNA processing

Histones H2A, H2B, H3 and H4 form the core of a nucleosome and thus are called core histones.
Processing of core histones is done differently because typical histone mRNA lacks several
features of other eukaryotic mRNAs, such as poly(A) tail and introns. Thus such mRNAs do not
undergo splicing and their 3'-prime processing is done independent of most cleavage and
polyadenylation factors. Core histone mRNAs have a special stem-loop structure at 3-prime end
that is recognized by a stemloop binding protein and a downstream sequence, called histone
downstream element (HDE) that recruits U7 snRNA. Cleavage and polyadenylation specificity
factor 73 cuts mRNA between stem-loop and HDE.

Histone variants, such as H2A.Z or H3.3, however, have introns and are processed as normal
mRNAs including splicing and polyadenylation.

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Ans 5: A living organism requires energy simply to survive as an organized structure, let alone to
perform any useful functions. In this section we explore the chemistry of the major source of the
energy used by animals, the oxidation of glucose.

Biochemical, or living, systems require sources of energy. The fundamental source of energy for
them is light, whose source is the sun. A small fraction (for sugar cane, 8% of incident light; for
corn, 1 - 2%) of this light can be used by plants, through photosynthesis, to obtain compounds
from carbon dioxide and water. The sugar glucose, whose molecular formula is C6H12O6, is
formed by the overall reaction

6CO2 + 6H2O C6H12O6 + 6O2(g).

Under standard conditions of 25o C and one atmosphere pressure, the standard free energy
change DGo of this reaction is +2870 kJ/mole. To make this non-spontaneous process go, 2870
kJ/mole must be supplied by energy from elsewhere, in this case light. The synthesis of glucose
may be taken as typical of the production of carbohydrates, or even of organic compounds
generally, in plants.

Animals, such as human beings, are not capable of photosynthesis and so they derive their
energy by running reactions such as this backwards, degrading the glucose to, ultimately, carbon
dioxide and water. The overall reaction of glucose oxidation is the reverse of the overall reaction
for its formation. Fot he reverse reaction the standard free energy change DGo must then be
-2870 kJ/mole.

Consider a somewhat typical biochemical reaction carried out by the enzyme

phosphoglucomutase, or PGM: glucose-1-phosphate (G1P) --> glucose-6-phosphate (G6P). If we
start with a solution of glucose-1-phosphate (G1P) of physiological concentration, say 0.02
molar originally, and carry out the reaction using the enzyme, then we observe, after the reaction
has finally come to equilibrium, 0.019 molar G6P and 0.001 molar G1P. A free energy change of
2870 kJ/mole is obviously much too large, as the calculation below shows:

K = [PRODUCTS]/[REACTANTS] = 0.019/0.001 = 19, and

DGo = -RT ln K = -2.303 RT log 19 = -7.30 kJ/mole

The oxidation of glucose actually takes place in a complicated series of steps involving ATP
(adenosine triphosphate, the energy carrier of living organisms), ADP (adenosine diphosphate, a
lower-energy form of ATP; ATP + H2O --> ADP + H2PO4-, with DGo= -30.54 kJ/mole), NAD+
(nicotinamide adenine dinucleotide), and NADH (the reduced form of NAD+). These steps occur
as in three groups.

First come the glycolysis steps, for which DGo = -196.6 kJ/mole. These steps carry out the
overall reaction:

C6H12O6 + 2ATP + 2ADP + 2NAD+ 2NADH + 4ATP + 2 lactic acid

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The structure of lactic acid is CH3-CHOH-COOH and its systematic name is 1-
hydroxypropanoic acid. Two molecules of lactic acid are produced, and two molecules of ATP
are produced from ADP, on glycolysis of a molecule of glucose.

The NADH produced in this reaction is recycled. This is the purpose of the second portion of the
pathway, the oxidation steps, which provide recovery of the NAD+. These take place via the
cytochrome pathway:

2[3ADP + NADH NAD+ + 3ATP]

In the cytochrome pathway, there is a net loss of two molecules of NADH and six molecules of
ADP and a net gain of two molecules of NAD+ and six molecules of ATP. Overall, in the two
groups of steps considered thus far, there has been a net loss of one molecule of glucose and
eight molecules of ADP, and a net gain of eight molecules of ATP and two molecules of lactic
acid.

Third come the Krebs cycle steps:

2[CH3-CHOH-COOH + 6O2 + 15ADP 3CO2 + 3H2O + 15ATP].

In the steps of the Krebs cycle, two molecules of lactic acid are converted to six molecules of
carbon dioxide and six of water, while 30 molecules of ADP are converted to 30 molecules of
ATP.

Overall, the net reaction has been:

6O2 + C6H12O6 + 38ADP 38ATP + 6CO2 + 6H2O.

The overall energy of the exergonic (energy-giving) reaction,

6O2 + C6H12O6 6CO2 + 6H2O,

is -2870 kJ/mol, while the overall energy of the endergonic (energy-requiring) reaction,

38ADP 38ATP,

is 38 (+30.54) = +1160.5 kJ. The efficiency of energy transfer is then 1160.5/2870, or 40%,
under standard conditions. Under actual biological conditions it is somewhere between 44% and
66%.

The result of the complete oxidation of glucose is the production of 38 ATP/glucose, a

conversion efficiency of some 50% more or less. Most of this energy appears from the reactions
of the Krebs cycle. Some primitive organisms can use only glycolysis and so most of the energy
contained in glucose is not available to them.

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