Lecture 1 - Chapter 1

Biological structures in an organism serve a functional purpose, on the cellular and molecular level.

This concept applies for organelles as well, everything works together to achieve one function.

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There is a flow of energy through living systems  known as productivity. 

Productivity - the rate of formation of biomass in an ecosystem

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Living systems must have the ability to self replicate. Organisms, cells, down to molecules such as DNA

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Biomolecules are carbon compounds with H, N, and/or O

Hydrogen, oxygen, nitrogen, and carbon make up over 99% of atoms in the human body

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What properties of H,O,C,N make these atoms appropriate to the chemistry of life?

Their ability to form covalent bonds by electron-pair sharing

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Structural Organization of the complex biomolecules

Simple molecules are the units for building complex structures

Precursor -> metabolite -> Macromolecules/membrane -> Organelles -> Cells

• Precursor

  • Carbon dioxide
  • Water
  • Ammonia
  • Nitrogen
  • Nitrate

• Metabolites

  • Pyruvate
  • Citrate
  • Succinate

• Building blocks

  • Amino acids (to build proteins)
  • Nucleotides (builds nucleic acids -> DNA and RNA)
  • Monosaccharides (to create polysaccharides)
  • Fatty acids
  • Glycerol

• Macromolecules

  • Proteins
  • Nucleic acids
  • Polysaccharides
  • Lipids 

• Supramolecular complexes

  • Ribosomes
  • Cytoskeleton
  • Multienzyme complexes

• Organelles

  • Nucleus
  • Mitochondria
  • Chloroplasts
  • endoplasmic reticulum
  • Golgi apparatus
  • Vacuole

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Biomolecules have properties that reflect their fitness to living conditions

• Biomolecules and their building blocks have a sense of directionality

• Biomolecules contain information (this genetic or catalytic information)

• Biomolecules have characteristic 3D architecture (double helix)

• Weak forces maintain biological structures and determine the biomolecular interactions

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Forces

• Covalent bonds hold atoms together so that molecules can be formed
• Weak forces profoundly influence the structures and behaviors of the biomolecules
• Weak forces create interactions that are constantly forming and breaking under physiological conditions
• Energies of weak forces range from 0.4 to 30 kJ/mol

Weak forces

• Van der Waals interactions (0.4-4.0 kJ/mol)

  • Induced electrical interactions between approaching atoms/molecules

• Hydrogen bonds (12-30 kJ/mol)

  • Form between a hydrogen covalently linked to an electronegative atom and another electronegative atom

• Ionic interactions (20 kJ/mol)

  • Interaction between opposite charges

• Hydrophobic interactions (<30 kJ/mol)

  • Result from a tendency to exclude non-polar groups from water

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3D Architecture 

The 3D structure of biomolecules allow them to specifically interact with other biomolecules 

Biomolecules are only functionally active within a narrow range of environmental conditions

Weak forces to stabilize and interact with biomolecules to fulfill their functions 

The biomolecular recognition is mediated by weak chemical forces, which restrict organisms to narrow range of environmental conditions 

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Organization of cells 

Prokaryotic - a single plasma membrane, no nucleus or organelles 

Bacteria or Archaea

Eukaryotic - much larger in size (1000-10000x larger than prokaryotic). Contains membrane bound organelles such as nucleus, ER, Golgi, mitochondria, etc. 

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Viruses 

Viruses are supramolecular complexes of a nucleic acid encapsulated in a protein coat 

• Viruses are NOT alive
• Viruses are NOT cellular 
• The are not cell sustaining systems
  • They need a host to replicate
  • They need a host to survive
• Viruses can not function on their own

Viruses can cause disintegration of the cells they infected or they can integrate into the hose chromosome and become quiescent (lysogeny)

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Lysogeny - type of life cycle that takes place when a bacteriophage infects certain types of bacteria. 

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==Active Recall Questions==

What are the distinctive properties of living systems?

• Living systems serve a distinct function, and they work together with other systems to produce and optimize the fitness of a certain organism. The wing of a bat, for example. Down to the molecular level the living systems are working to fulfill that function.

What kinds of molecules are biomolecules

• Biomolecules are molecules that contain carbon, oxygen, hydrogen, and nitrogen. In the human body these 4 atoms make up 99% of the human body. These molecules are able to readily form covalent bonds and interact with each via weak bonds and forces. 

What is the structural organization of complex biomolecules

• (in)organic precursors -> metabolites -> macromolecules and membranes -> organelles -> cell

How do the properties of biomolecules reflect their fitness to the living condition

• The ability for these biomolecules to interact with one another via strong forces (covalent bonds) and weak forces (Hydrogen bonds, van der waal interactions, ionic interactions, hydrophobic interactions)
• The 3D structures of biomolecules such as lock and key of enzymes also increase the efficiency of these biomolecules

What is the organization and structure of cells

• Cells are divided into two categories:
  • Prokaryotic - single plasma membrane, no nucleus or organelles
  • Eukaryotic - membrane bound organelles such as the nucleus, golgi, mitochondria, etc. They are 1000-10000x larger than prokaryotic cells.

What are viruses?

• Viruses are NOT cells 
• They require a host to sustain their life
• They are not self reliant
• Viruses are supramolecular complexes of a nucleic acid encapsulated in a protein coat