Biology for Engineers

Discussion 1
Submitted by: Date of Submission: 01/10/2017
Abhishek leve
APE-GAS
Sap ID: 500045994
Enrollment no: R820215005

1. Questions to be answered:
1. Which organelles constitute the cytoskeleton and how (3)
2. Can we perform the translation of amino acids in laboratory? Justify your answers. (5)
3. DNA is double stranded. What would happen if it was single stranded? (2)
4. Hydrogen bonding is the basis of life. Justify (5)

Ans 1:
1. Cells need to keep their shapes intact and this is done via cytoskeleton.
2. Cyto means cell, therefore, cytoskeleton means cells skeleton.
3. Cytoskeleton is the framework of cell. It is highly organized & also flexible.
4. It functions nearly same as body skeleton where it provides structural support so the cell can keep its shape,
move around and be protected from outside sources.
5. The effect of outside forces on cell is called mechanical sources and the cytoskeleton helps to resist the
change in shape of a cell due to mechanical stresses.
6. It gives support to the cell membrane, helps evenly split up chromosomes during cell division and aids in
recovery from any outside injury.
7. It is also involved in organelle trafficking which is the movement of cell components like mitochondria from
one part of the cell to another.
8. The components of cytoskeleton are not found single stranded but are composed of multiple strands of 3
main components.
9. In addition to 3 main components, there are accessory proteins that aid in cytoskeletal assembly,
disassembly, stability and cellular transport.
10. The 3 main components of cytoskeleton:
i) Microtubules
ii) Intermediate filaments
iii) Micro filaments
11. Microtubules: They are largest in size. They are small, round hollow tubes and have a diameter of about 24
nanometer. They are made up of protein called tubulin. 13 tubulin connects to form a tubulin. They are very
dynamic in nature as they can easily change, they are constantly growing or shrinking. They are involved in
transport of cellular materials and divvying chromosomes during cell division.
12. The middle or intermediate sized component of cytoskeleton are the intermediate fluids. Intermediate
filaments in contrast to microtubules and microfilaments are made up of many different types of proteins
that are strung together into polymers and then these polymers twist together to make the intermediate
filaments. They provide support to the cell or helps to resist the mechanical stress.
13. Micro filaments are the narrowest. They function in cellular movement, have a diameter of about 7 nm, and
are made of two intertwined strands of a globular protein called actin. For this reason, microfilaments are
 also known as actin filaments. Microfilaments also provide some rigidity and shape to the cell. They can
depolymerize and reform quickly, thus enabling a cell to change its shape and move.

Ans 2:
Yes, it can be performed in the laboratories with the use of biotechnology engineering by performing the
translation inside a prokaryotes and giving them the specific environmental conditions like PH, temp, enzymes.

Arrangement of amino acids in a line specific sequence and formation of polypeptide chain according to the
specific sequence of information written on m-RNA is called translation. It occurs in cytoplasm.
Primary requirements for translation are:
1) Ribosomes m-RNA
2) t-RNA
3) enzymes
4) Amino acids
5) ATP
6) GTP
7) Specific activators
The process of Translation involves:
i) Activation of amino acids & its transfer to t-RNA: amino acids are activated by ATP in the presence
of an enzyme known as amino acyl synthetase (ACS) and linked to the cognate t-RNA a process called
as charging of t-RNA or amino acyl action of t-RNA as a result amino acyl t-RNA is formed which moves
towards ribosome.
AA +ATP + Enzyme (ACS) AA + AMP+ Enzyme complex + PP (pyrophosphate)
AA - AMP - Enzyme complex + t-RNA AA t-RNA complex + AMP + amino acyl t-RNA

ii) Initiation of polypeptide chain: AUG is the initiation codon for m-RNA. It codes for methionine.
Formyl group is attached to free amino group of methionine. The t-RNA bringing formyl methionine is
called f-met t-RNA and it acts as initiator. As the anticodons of t-RNA are complementary to the codons
of m-RNA, they can develop or loose hydrogen bonds with codons of m-RNA.
Ribosomes have 2 sites for t-RNA: (a) Amino-acyl or acceptor site. (b) Peptidyl site in the larger sub
unit. Aminoacyl t-RNA first binds to A-site of ribosomes & move to P- Site while initiator t-RNA first
binds to P side. The initiator amino acyl t-RNA in the presence of m-RNA combines with sub units of
ribosomes. This process requires energy.

iii) Elongation of polypeptide chain: Chain elongation takes place by the establishment of peptide bonds
between the amino acids as the ribosomes move along m-RNA one codon at a time in 5to 3direction.
Depending on the second codon of m-RNA, the t-RNA with anticodon complementary to the codon of
m-RNA forms a complex with the corresponding activated amino acids and move to the ribosome and
binds to the A-site. This is facilitated by elongation factor & energy in the form of GTP. Formyl
methionine in P-site establishes a peptide bond with the second amino acid at A-site. Polypeptide chain
grow from C to N direction. Peptide bond is catalyzed by the enzyme peptidyl transferase.
After the bond formation, ribosomes moves to the nest codon of m-RNA and this is called translocation.
Translocation requires translocase and GTP. Therefore, aminoacyl t-RNA enters A-site and moves to P-
site after developing peptide bond.

iv) Chain termination on activation of amino acids: When the terminating codons UAA, UAG or UGA
present in m-RNA, it indicates the end of polypeptide synthesis. They do not code for any amino acid
and hence no amino acid enters A-site and thus they act as stop signals. At the end, a relative factor
 binds to the stop codon, terminating translation and releasing the complete polypeptide from the
ribosome.

Ans 3:
If DNA is single stranded then it will be less stable than double stranded DNA which will lead to mutation. The
'information' part of DNA is the nitrogenous base, as opposed to the pentose sugar or the phosphate residues.
In a single-stranded molecule, this important part would be exposed to the cellular environment, providing
more opportunity for it to be mutated by the various chemicals there. In a double-stranded configuration,
however, the two nitrogenous bases are locked within the complex, facing each other in the center of the
molecule. This organization helps to safeguard them from local mutagens.

Secondly, having two complementary strands facing each other fundamentally means having two copies of the
same thing placed right next to each other. This allows for proof-reading.

Lastly, Double stranded are supposedly more stable to heat denaturation or pH variations compared to single
stranded DNA in higher organisms. However, single stranded circular DNA have been predominant in certain
family of viruses such as geminiviridae (Gemini viruses), microviridae, or in certain bacteriophages such as phi
X 174 etc. Surprisingly such single stranded circular DNA viruses are present in aqueous, extreme habitats.

Ans 4:
Throughout bio-chemistry, there are many bonds without which life as it on earth would not have been conceivable.
One of these bonds is the hydrogen bond, a fragile chemical bond that exist in indispensable biological molecules
such as water (H20) & polypeptides. Campbell and Reece defined hydrogen bonding as stirring when a hydrogen
atom is covalently bonded to an electronegative atom but enticed to another electronegative atom.

A hydrogen bond is comparatively weaker than covalent and ionic bonds, as much as 22 times weaker. So in order
to describe why hydrogen bonds are so essential, perhaps it is not substantial to that hydrogen bonds are weak on
their own, since the majority of their use within strong structure is facilitated by their strength as a large number of
hydrogen bonds. For example, the fundamental strength of tendons and skin lies within the many hydrogen bonds
in the collagen protein.

For formation of collagen, the strength of hydrogen bonds is required to firstly join 2 amino acid chains together to
form helix. Three helices are then bound into a triple helix by yet more hydrogen bonds. The result is a fibrous
quaternary protein structure with a high tensile strength that the mammalian skeletal muscles could not function
without. Tendons attach skeletal muscles to their respective bones and we would simply not be able to move without
them. Other use of hydrogen bonds in proteins include contributing to the specific conformational shape of globular
proteins, called protein folding.

A precise 3D shape is required in most enzymes so that the shape of binding site is complementary to the chemical
reacting with the enzyme. Hydrogen bonds are essential along with ionic bonds, covalent bonds, disulphide bond
and hydrophobic interactions, for making secondary structure (i.e. helices and pleated sheets) coil into a tertiary
structure. A tertiary structure or a quaternary structure after further protein folding, can then be utilized as a specific
enzyme within organism to carry out specific metabolic reactions.

It is the hydrogen bond found in water that makes the metabolic reactions in the human body so efficient. The slight
increase of strength between water molecules cause by hydrogen bonds means that in comparison to other fluids
without hydrogen bonds, water requires a lot of energy to raise the temperature of it. This is called heat specific
capacity, an attribute that is especially useful when the body is actively maintaining the body temperature at 37C.
For metabolic reactions this is very useful because it means that the enzyme can work at their optimum temperature,
often the same as 37C and thus the metabolic reactions in the body are very efficient. For every 10C below optimum
temperature, the rate of successive substrate enzyme collisions decrease by 2 to 3 times. The high heat capacity of
water is one of several hydrogen bonding attributes that benefit the marine environments, unsurprisingly, with the
high surface tension and the small relative density of ice also playing a large role in how aquatic organisms survive.

Transpiration is the loss of water from the leaves of plants by evaporation and causes water to move into the roots
up vascular tubes within in the plant stem. This means a plant can transport water around its tissues for use in
respiration and other metabolic reactions. Hydrogen bonds play a large role in transpiration in the same way as they
do in the cohesion of water molecules to cause high surface tension. When the water molecules are moved up the
xylem vessels, they move as a whole due to in the cohesive forces between the molecules. The molecules also stick
to the walls of the vessels by hydrogen bonds, aiding the transport of the water furthermore.

Concluding, it is clear to see that without hydrogen bonds, life, as we know it today would not exist.