Properties of Biomolecules Reflect Their Fitness to the Living Condition

Living systems utilize energy and simple molecules from their surroundings to produce complex molecules and molecular assemblies. These assemblies have varied functionalities, are lower in entropy than the raw materials from which they were produced, and can only be achieved with the input of energy from the surroundings:

• Cells are "open" thermodynamic systems that exchange both energy and matter with their surroundings

Living systems require molecules that have the ability to provide functionalities associated with:

• The utilization of outside energy sources to be applied towards work, heat regulation, and entropy reduction
• Replication and communication (both involve information, therefore, related to entropy reduction)

• Living systems do not violate the laws of thermodynamics. But they do require the input of energy from their surroundings.

Living systems make use of polymeric molecules

• Proteins are linear polymers of amino acids. There are 20 common amino acid monomer building blocks.
• Nucleic acids (deoxyribonucleic acid - DNA, and ribonucleic acid - RNA) are linear polymers of nucleotides. There are 4 common DNA monomer building blocks.
• Polysaccharides are linear or branched polymers of carbohydrates

Important characteristics of these complex polymeric molecules include their directionality and composition (i.e. the nature of the sequential order of the individual different types of monomeric units). This is not unlike the way letters are used to make words:

• DR BLABER IS UNDERPAID (only this has true meaning)
• DIAPREDNU SI REBALB RD (same letters backward have no meaning and is of interest only to those on drugs)
• A SCRABBLE DIP DRIED ON TOUR (an alternative arrangement of letters has a different meaning)

The "start" and "end" of such polymers as proteins and DNA are defined by the location of particular functional groups

• The start of a protein polymer is called the "amino terminal", and the end is called the "carboxyl terminal"
• The start of a nucleic acid polymer is called the "5-prime" terminal and the end is called the "3-prime" terminal

Biological polymers, principally proteins, but also nucleic acids, can fold up into a unique three-dimensional structure

• Such three-dimensional structures are often called the "native" or "folded" conformation of the polymer
• The "unfolded" conformation is like a piece of well-cooked spaghetti - it has no defined structure, and is best described by an ensemble of possible conformations (an ensemble of random conformations)
• The "native" conformation is a single, unique conformation.

The native conformation (or "native state") of a biological polymer has the following general features:

• It represents a global energy minimum (i.e. it does not violate the laws of thermodynamics). The entropic cost of limiting the polymer to a single conformation is offset by the enthalpic gain of forming numerous non-covalent interactions between various functional groups between the monomeric units in the polymer. Solvent affects may also contribute to the stabilization of the native conformation.
• The structure of the native conformation confers either a physical or chemical functionality, or an information-storage role, upon the polymer
• Due to their shape, folded polypeptides can recognize and bind to each other (resulting in molecular communication). This is not possible with the unfolded conformation(s).
• A loss of the unique native conformation will also destroy the functionality of the polymer - the unfolded state(s) have lost all functionality
• Non-covalent interactions stabilize the structure. Increasing thermal motion can overwhelm non-covalent interactions. Therefore, increasing temperatures can result in a loss of the native conformation of proteins or nucleic acids (this phase transition is often called "melting" of the polymer structure)
• As long as the polymer does not suffer a break in a covalent bond, the native structure can often be recovered upon removal of thermal motion (i.e. by cooling).

Van der Waals attractive forces

• Dipole - dipole (strength is proportional to 1/r³)
• Dipole - induced dipole (strength is proportional to 1/r⁵)
• Induced dipole - induced dipole, also known as "London dispersion forces" (strength is proportional to 1/r⁶)
• All molecules can participate in dispersion forces. Although they are the weakest of the van der Waals forces, they are typically more numerous than the other forces, and therefore, add up to a significant attractive force.
• Due to the 1/r⁶ relationship to strength, meaningful dispersion forces arise when neighboring molecules pack well together - that is to say, structural complementarity (i.e. like pieces of a jigsaw puzzle)

Van der Waals repulsive forces

• If atoms get too close, their electron clouds repel each other (strength is proportional to 1/r¹²)

Hydrogen bonds (H-bonds)

• A unique type of dipole-dipole bond in which molecules contain a Hydrogen that is covalently bonded to a more electronegative element such as O, N or Cl (commonly O or N)
• The valence electron of the hydrogen in the bond is withdrawn towards the O or N, leaving a "naked proton"
• Non-bonding electrons in another N or O group can get very close to the hydrogen, and form a strong partial electrostatic interaction
• Water-water and water-biological polymer interactions are mediated by H-bonds

• H-bonds are stronger than van der Waals interactions, but weaker than ion-ion interactions

Ionic interactions

• Typically involve negative carboxyl groups and positive amino groups or metal cations
• The strongest type of non-covalent interaction

Red indicates contributions to van der Waals interactions

Hydrophobic Interactions

This is not a fundamental type of interaction, but is based on issues of solvent-solute interactions and entropy

Why don't water and gasoline mix?

• Gasoline (octane; a hydrocarbon) can only participate in dispersion forces
• Water molecules can form much stronger hydrogen bonds between each other
• It takes a lot of energy to disrupt the water molecules to make room for the octane molecules (lot of energy expended). However, the interaction between water and octane is via much weaker dispersion forces, thus, you pay a big energetic cost to separate the water molecules and don't recoup much energy when the octane is dispersed
• The entropic gain in dispersing the octane molecules is not enough to overcome the energetic cost of disrupting the water-water interactions

This situation is relevant to biological polymers that contain aliphatic or aromatic carbon groups. What happens when they are placed in water?

• Due to the presence of O, and N groups, such polymers are soluble, however, water will not hydrogen bond with aliphatic or aromatic groups. Therefore, solvent will form an ordered clathrin cage around carbon groups and this is entropically costly
• If the polymer adopts a conformation that sequesters the aliphatic and aromatic groups from solvent, then the solvent that was ordered around these groups is released and once again becomes part of the disordered bulk solvent. This results in an entropic gain and is therefore a spontaneous process (i.e. a lower free energy state)
• This hydrophobic interaction between water and carbon-containing groups can contribute a large driving force for the formation of structure in biological polymers and assemblies. Again, the effect in question is based upon the entropic gain of solvent molecules as they go from being ordered around hydrophobic groups to being free in bulk solvent when the hydrophobic group is removed from the solvent environment (more details in the next lecture)

Consequences of unique molecular structures adopted by biological polymers

• "Lock and Key" or molecular complementarity can be used to communcate information, to bring about complex macromolecular assembly, to cause conformational changes, or to produce chemically-reactive structures
• Enzymes are proteins that are chemically reactive catalysts, due to their unique structure. Metabolic regulation is achieved by enzymes.
• Since non-covalent forces maintain such structures, structure can be perturbed or disrupted in response to changes in temperature, pH, ion concentrations, pressure, or other environmental conditions, thus, function can be modulated

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Organization and Structure of Cells

Prokaryotes - no nucleus (they do have genetic material, its just not present in a separate compartment within the cell!)

Eukaryotes - have a nucleus, and other membrane-bound organelles within the cell. (You are a eukaryote. Congratulations...)

• Sequencing of the human and bacterial genomes reveals that diverse life forms on earth share similar biochemical molecules (e.g. the proteins in bacteria can share a high degree of amino acid identity with homologous enzymes in humans)
• All life forms share similar metabolic pathways

 

Some differences between Eukaryotes and Prokaryotes

Prokaryotic cells	Eukaryotic cells
No nuclear membrane: chromosome(s) in direct contact with cytoplasm	Chromosomes are enclosed in a double layered nuclear membrane
Simple chromosome structure	Complex chromosome structure; DNA associated with histone proteins
Cell division does not involve meiosis	Cell division involves mitosis and meiosis
If present, cell walls contain peptidoglycan, no cellulose or chitin	If present, cell walls contain cellulose or chitin, never peptidoglycan
No mitochondria or chloroplasts	Mitochondria usually present, chloroplasts in photosynthetic cells
Cells contain ribosomes of only one size	Cells contains two types of ribosomes, one in cytoplasm, and smaller type in mitochondria
Flagella, if present, have a simple structure	Flagella, if present, have complex structure

 

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Viruses

What are viruses and are they "alive"

• Viruses are not cells, but rather, are complex macromolecular assemblies that contain genetic material (i.e. polynucleotides)
• Viruses gain entry into a host cell (either eukaryote or prokaryote) via specific molecular recognition of the surface of the cell
• The virus uses the host cells molecular machinery to make more viruses (i.e. make more viral polynucleotide and any necessary assembly molecules
• The viral progeny (i.e. newly made viruses) are released either by breaking open the host cell (a lethal event for the cell) or by some form of secretion (not necessarily lethal to host cell)
• Host cells are impaired or destroyed by viral infection. Sometimes the "impairment" results in a cancerous cell. Either way, viruses are usually not good news for the host cell.
• Some viruses infect a host cell, integrate its own genetic material into the host, and stays "dormant" for many years (this is called "lysogeny"). Later on, it enters a cycle of viral replication and destruction of the host cell.
• Another word for virus is "phage". A "bacteriophage" infects bacterial cells.
• Viruses are typically host-specific, but this can change and can be really nasty since the new host will have no immunity. This is a real problem in areas where humans and animals live in close proximity. It is no surprise that new strains of influenza, that have "jumped" from chicken or pig to humans, arise in regions where such animals and humans live in crowded conditions.
• Virologists are the most paranoid people on earth (next to pre-tenured faculty) - many believe it is only a matter of time before the next viral pandemic hits. Many virologists have second homes deep in the mountains (hard to get to and well defended...).
• Viruses appear to have evolved in tandem with the cells they infect, and may well represent renegade genetic material from these hosts. Sort of like a "Junkyard Wars" of the biological world.

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