Evaluate the importance of shapes that fit together in cells and organisms (25

marks)

The binding, changing and specificity of shapes is of paramount importance in all biological
organisms, both on a unicellular and multicellular level in all classifications of organisms.
Enzymes, a crucial component to a multitude of biological pathways, are reliant on the
substrates being complementary to active sites which enable reactions such as
photosynthesis to occur. Photosynthesis is a key biochemical process that occurs in the
chloroplasts of many plants such as dock leaves and rhubarb. In the light-independent stage
of photosynthesis the Calvin cycle takes place inside the stroma of chloroplasts. The Calvin
cycle combines a molecule of carbon dioxide (CO2) with ribulose bisphosphate (5C) to
synthesise two molecules of glycerate 3-phosphate (GP). This reaction pathway would not
take place without the presence of Rubisco which is an enzyme that relies on the
complementary nature of substrates to an active site with specific tertiary protein structure.
For example, CA1P (2-carboxyarabinitol-1-phosphate) is a competitive inhibitor which
modifies the shape of the active site of Rubisco. This would halt the production of hexose
sugars such as glucose in photoautotrophic organisms which would prevent organisms
further up the food chain, such as grasshoppers in the Everglades or ruminants such as
cows, sheep and deer from acquiring glucose which is an essential reactant in the
respiration biochemical pathway.

Respiration is an essential biochemical process which synthesises ATP from glucose, the
basic energy molecule found in almost all organisms. In mammalian organisms respiration
could not occur without glucose or O2 which depends on the shape-specific quaternary
structure of a globular haemoglobin polypeptide. Haemoglobin is a four-chained polypeptide
that is found inside the red blood cells of many mammals, such as humans containing four
O2 binding spots or ‘ferrous’ groups. These are specific shapes that fit four Oxygen
molecules per haemoglobin molecule which facilitate the aerobic respiration biochemical
pathway. Aerobic respiration requires oxygen in order to undergo oxidative phosphorylation,
where H+ ions from chemiosmosis move from intermembrane space up ATP synthase
(another form of enzyme dependent on shapes) by proton motive force and combine with O2
from haemoglobin and electrons from the electron carrier chain. This results in the
combination of ADP + Pi to form ATP and a water molecule at the terminal electron acceptor
(oxygen). If haemoglobin did not have a specific shape that is not only able to carry oxygen,
but also alter affinity for oxygen at varying partial pressures to optimise the rate of aerobic
respiration organisms such as humans and other mammals simply could not synthesise
enough ATP for major activity such as muscle contraction and metabolic processes such as
macromolecule synthesis and active transport.
Inter-membrane movement of biological molecules is an underpinning process that enables
all organisms to function. Active transport is a process that requires ATP originating from
glycolysis and the tricarboxylic acid (Krebs) cycle. Active transport is the movement of
substances against a concentration gradient, supplemented by the hydrolysis ATP through a
carrier protein. Carrier proteins are a specific shape to various substrates which enables the
survival of organisms. An example of this is the Na+/K+ pump inside the ileum of a human
small intestine, where sodium ions are actively transported out of the ileum cell through a
carrier protein into the blood and potassium ions are pumped in. This causes the facilitated
diffusion of sodium from the small intestine through a channel protein, which has a specific
shape to facilitate this process, driving the absorption of a significant concentration of both
glucose and amino acids against a concentration gradient, allowing for processes such as
respiration and protein synthesis to continue which are vital for cell growth through mitosis
and metabolic processes. Furthermore, active transport is vital to the process of lactose
transport in prokaryotic organisms such as the bacterium E.Coli which use a proton (H+)
gradient in order to drive lactose uptake through a carrier protein. Endocytosis, the process
by which material is internalised by being surrounded by cell membrane and absorbed,
heavily relies on shapes. This can be seen in phagocytes which use pseudopodia to create
specific shapes which envelope viral proteins such as HIV which facilitates cell-mediated
immune response.

The immune system is a key component of most mammalian organisms, comprising T cells,
B cells and phagocytes such as macrophages to name a few which enable cell-mediated
and humoural immune response. Shapes are instrumental in primary immune response as
they dictate the interaction between attachment proteins and antigens which allows for
antigen recognition by specific T cells in cell-mediated response. This is illustrated clearly in
the immune response to COVID-19 where a SARS-CoV-2 S protein is bound to an ACE2
receptor on the cell-surface membrane of a COVID-specific T-cell. The complementary
shape of the ACE2 receptor enables the correct T cell to release cytokines which then do
pleiotropic activity on specific receptors of B cells. This stimulates humoral response which
enables the differentiation of B cells to plasma cells which can secrete vast concentrations of
antibodies that are specific to the COVID-19 virus. The antibodies have a specific tertiary
structure that complements the structure of the viral proteins, which enables the
agglutination and, consequently, the phagocytosis of COVID-19 particles by macrophages
which hydrolyse the particles using hydrolytic enzymes that fit together with viral proteins
inside vesicles, destroying the virus. These products are then secreted into the bloodstream,
where processes such as protein and DNA synthesis can utilise them around the body.
The congregation of specific shapes and enzymes is illustrated no better than in protein
synthesis, a fundamental process in mitosis which occurs in all mammals. Protein synthesis
starts with the transcription of mRNA from DNA that codes for a specific polypeptide subunit
in an organism. This process heavily relies on shapes as enzymes such as DNA helicase
which is specific in shape to the hydrogen bonds between opposite nucleotide pairs,
hydrolysing hydrogen bonds which isolates individual strands of DNA; as well as RNA
polymerase which synthesises phosphodiester bonds between the specific sugar-phosphate
shapes that make up the phosphate backbone of an mRNA molecule. Furthermore, the
organic bases themselves: adenine, uracil, thymine, guanine and cytosine, are the
fundamental building blocks of genetics and rely heavily on complementary pairing in order
to prevent mutation and allow for genetic continuity between species across thousands of
years. tRNA, another critical component of the life cycle of cells, is also reliant on 3D shape
in order to preserve the phenotype of an organism. In the cell cytoplasm, an mRNA molecule
binds to a ribosome and begins the process of translation, where a START codon is read,
kickstarting the process. A tRNA molecule with an anticodon complementary in shape to the
codon of the specific locus on the mRNA molecule binds, attaching the corresponding amino
acid in the correct location. This process continues and allows for the production of a vast
array of polypeptide chains through only variance in primary structure, all of which arise from
only 20 amino acids. Hence, shape in biology allows for continuous production of a vast
array of polypeptides, leading to a huge range of organisms on Earth; from lugworms,
unicellular amoebae and viruses just nanometres wide to vast elephants, giraffes and all
those that fall in between.