Carbon, Plants, and Life's Value

• Dr. Scott Napper is a Professor in the Department of Biochemistry at the University of Saskatchewan.
• He is also a Senior Research Scientist at the Vaccine and Infectious Disease Organization-International Vaccine Center.

Biochemistry Definition

• The discipline studies life down to the molecular level.
• It applies chemical philosophies to explain biology.
• The study of the molecular logic of life.
• Underlying common reactions and principles for all living organisms.

Unity of Biochemistry/Life

• Living organisms are remarkably uniform at the molecular level, despite differences size and complexity.
• All organisms use a core of essential biochemical processes.
• All organisms use a common repertoire of building blocks to create biomolecules:
  • Nucleic acids
  • Proteins
  • Polysaccharides
  • Lipids

Foundations of Life

• Living state can be considered on the basis of:
  • Chemical composition
  • Energy
  • Genetics
  • Evolution

Chemical Foundations

• Living things are made from simple, common ingredients.
• The four elements: carbon, oxygen, hydrogen, and nitrogen account for 98% of most organisms.
  • Water accounts for much of the oxygen and hydrogen in living things.
  • All known life forms are carbon-based.
• The chemical elements within the biosphere are readily available with:
  • Carbon coming from the air through plants (ability of plants).
  • Oxygen from the air.
  • Hydrogen from water.
• The air contains lots of nitrogen but in an inert form (N2), which is not readily available.
• Nitrogen within the biosphere comes from plants, extracting it from the soil.
  • The availability of nitrogen in soil often limits plant growth, therefore impacting food production.
• The amount of naturally occurring nitrogen in soil would enable enough food for about 4 billion people.
• In 1972, the chemicals within a human body had a worth less than a dollar.
• Tissues, organs, and biomolecules within a human being are valued at $45,000,000.
• Chemicals are not exotic but how they come together is priceless.
• Carbon based because it is extremely versatile in terms of the number and variety of chemical bonds that it can form.
• Silicon is the "next-best" candidate as a chemical foundation for life: Silicon can also form four covalent bonds and is abundant in the Earth's crust.
• Carbon-to-carbon bonds are stronger than silicon-to-silicon bonds (more stable biomolecules).
• Combustion of carbon-carbon bonds releases more energy.
• Combustion products of carbon (carbon dioxide) are soluble in the biosphere for recycling.

Molecules and Functional Groups

• Different functional groups are unique with respect to their size, shape, charge, reactivities, and hydrogen-bonding capacity.
• Functional groups determine the structure, function, and properties of the biomolecule.

Biomolecule Structure and Function

• For all biomolecules, structure dictates function.
• Biomolecules "do what they do" because of their structures.
• Understanding the structure allows for prediction of function, including molecular function, and understanding complex biology and development of treatments.
• Conformation is the flexible spatial arrangement of atoms within a molecule (can be changed without breaking covalent bonds).
• Configuration is the fixed spatial arrangement of atoms within a molecule (cannot be changed without breaking covalent bonds).
• Configuration is conferred by either double bonds or chiral centers.
• Geometric (cis-trans) isomers have the same chemical formula:
  • They differ in the configuration of groups with respect to a non-rotating double bond.
  • Cis: "on this side" groups on the same side of the double bond.
    • Trans: "across" groups on opposite sides of the double bond.
  • Geometric (cis-trans) isomers can have very different biological properties.
• A chiral carbon has four different substituents attached.
  • groups may be arranged in different ways in space yielding two stereoisomers that differ in their configuration.
  • Chemical properties of stereoisomers tend to be identical, biological properties can be distinct.
• Biomolecules often constructed exclusively from one stereoisomer.
  • Proteins are built entirely from L-Amino acids.
• Interactions between biomolecules are stereospecific.

Complex Molecules

• Biomolecules are often polymers of simple building blocks.
  • The structure and function of the resulting biomolecules are more complex than their precursor molecules.
  • The whole is greater than the sum of the parts.
• Advantages of constructing biologicals as polymers:
  • Simplicity: Simple and conserved reactions for synthesis and degradation.
  • Recycling: Biomolecules can be digested back to component building blocks which are reusable.
  • Diversity: Complex molecules can be generated.
• There are four major classes of biomolecules:
  • Proteins
  • Carbohydrates
  • Nucleic Acids
  • Lipids
• Proteins are linear polymers of amino acids:
  • There are 20 amino acids total.
  • Amino acids link together to form linear chains that fold into complex patterns with distinct biological activities.
• Polysaccharides are monosaccharides which are linked together to form linear or branched polymers.
  • Higher order polysaccharides have important biological roles relating to structure energy storage, and cellular recognition.
• Nucleic Acids are linear polymers of nucleotide building blocks (5 building blocks for DNA and RNA).
  • Acids are involved in all aspects storage and utilization of genetic information.
• Lipids are aggregates (rather than defined polymers) of building blocks. Lipids serve in energy storage, formation of membranes, and signalling.
• There are two basic classes of living organisms; prokaryotes and eukaryotes.

Prokaryotes vs Eukaryotes

• Prokaryotes
  • Small (~ 1µm diameter), simple, single cell organisms (such as bacteria).
  • Rapid growth allow quick adaptation to changing environmental conditions.
  • They have a nucleoid, which contains nucleic acid.
• Eukaryotes
  • Large (~100 µm diameter) of complex cells.
  • Make up multi-cellular organisms such as yeast, plants, fungi, vertebrates.
  • Organelles support specialized functions.
  • There is differentiation of cells to unique and specialized cell types.
• Approximately 30 trillion eukaryotic cells are in the human body with another ~100 trillion prokaryotic cells.
• The prokaryotic cells are critical to our health.
  • Bacteria in the gut help digest food, help maintain immune system
• Brain in the gut which includes microflora, may effect mental health.
  • Possible ways to influence the microbiota include diet, pro and prebiotics, and fecal transplants.
• There are two experimental approaches:
  • In vitro studies the behaviour of molecules outside the context of the cell and organism.
  • In vivo studies occur within the complexity of the cell or organism.
  • Experiments which are successful in vitro often fail in vivo.
• Being alive is energetically expensive, this energy must be obtained from the environment.

Thermodynamics in Biology

• In BMSC230 you will study (in quantitative and chemical terms) the means by which energy is extracted, channeled, and consumed in living cells.
• Cellular energy conversion can be considered in the context of the laws of thermodynamics.
  • In any physical or chemical change, the total amount of energy in the universe remains constant, although the forms of the energy may change.
• Living systems and their biomolecules require organization.
• Energy transducing is the conversion of energy of metabolized nutrients, or the energy of the sun converting energy to work:
  • Work
  • Heat
  • Generation of complex biomolecules

Gibbs Free Energy:

• This is from Willard Gibbs is energy changes that comes occur during chemical.
• Free energy (G) of any closed system is defined: energy associated with bonds.
  • Enthalpy (H): reflects the number and kinds of bonds.
  • Entropy (S): The degree of randomness.
  • Temperature: In degrees Kelvin.
  • The definition of free energy: G = H - TS
  • The free energy change: ΔG = ΔΗ - TΔS
• Non-spontaneous process- Energy input must occur in order to proceed (endergonic).
• Spontaneous processes releases free energy that be used. Exergonic to the point of equilibrium
• System that's in equilibrium- There will be no shift in energy.
• Cells can drive thermodynamically unfavorable reactions by coupling energy requiring (endergonic) to energy releasing (exergonic) reactions. If the sum of the free energy changes is negative, then overall process is exergonic (spontaneous).
• Energy extracts into the adenosine triphosphate(ATP) and serves as a "common" energy currency. ATP has a link between anabolic and catabolic reaction. - Catabolic- the breakdown build: -Anabolic- will the build

Genetic Foundations

• The perpetuation of life requires that genetic information be:
  • Stored, expressed & reproduced
• In many organisms, deoxyribonucleic acid (DNA) provides:
  • Instructions for cell to form w/ cellular components: Template for product formation with identical molecules that divides a cells. Two complimentary strands and linear polymer of building with a sequence that incodes information.
  • DNA has 2 complimentary strands
  • Each strand is polymer of 4 different types to its building blocks
  • DNA code based on linear sequence that holds all information
• Nucleotide sequence of genes is how amino acid is sequence from being correspond by sequence in DNA

Evolutionary Foundations

• When a organism is mutated in genetic mutation may appear in observable phenotype.
  • Survival of the fittest-
  • Changes made to hereitary that results in evolution.

Explore carbon's life-sustaining role and plant growth limitations. Learn about nutrient availability and notable advancements in food production. Understand differences between structural and stereo isomers.