Definitions of Life and Molecules

Conventional Definitions of Life

• Organization: Composed of one or more cells, the basic units of life.
• Reproduction: Ability to produce new organisms.
• Metabolism: Chemical processes necessary for life maintenance.
  • Catabolism: Breaking down substances to release energy.
  • Anabolism: Synthesizing substances using energy.
• Growth: Increased complexity from simpler to more complex forms.
• Homeostasis: Maintaining a constant internal environment.
  • Examples: Sweating to reduce temperature, shivering to increase temperature.
• Response to Stimuli: Ability to react to a stimulus.
• Adaptation: Ability to respond over time to environmental changes.

Other Proposed Features of Life

• Carbon Containing: Carbon forms the foundation of life on Earth.
• Reliance on Water: Water is essential for all life forms.
• Genetic Information: Uses DNA and RNA to store the blueprint for an organism.

What is a Molecule?

• Molecule: Smallest particle of a substance retaining its properties.
• Atom: Smallest particle of an element retaining its chemical properties; a molecule may be composed of one or more atoms

Molecular Characteristics of Life

• Thermodynamics: Life obeys the laws of thermodynamics.
• ATP: Common energy currency of life.
• Biological Molecules: Structure depends on similar biological molecules (e.g., proteins, lipids, carbohydrates, nucleic acids).

What is a Nutrient?

• Nutrient: Substance with nutritional value for an organism.
• Micronutrients: Required in small amounts (vitamins, microminerals).
• Macronutrients: Required in large amounts (carbohydrates, proteins, lipids).

Vitamins

• Act as cofactors for enzymes, and are organic compounds loosely bound to the enzyme during chemical reactions.

Nucleic Acids

• Essential for maintaining, growing, and repairing DNA and RNA.
• RNA is a messenger that carries instructions from DNA.
• RNA uses uracil instead of thymine.
• RNA is single-stranded.

Hydrocarbon Nomenclature

• Hydrocarbons: Chemical compounds containing only hydrogen and carbon.
• Alkane: Carbon-carbon single bonds.
• Alkene: At least one carbon-carbon double bond.
• Alkyne: At least one carbon-carbon triple bond.

Methods of Drawing Hydrocarbons

• Structural: Straight lines represent bonds.
• Condensed: Combines hydrogen atoms with carbons for simpler representation.
• Skeletal: Intersections represent carbon atoms.

Naming Linear Hydrocarbons

• Use prefixes to name hydrocarbons according to the number of carbon atoms present.

Atomic Structure

• Atoms have a central nucleus with protons and neutrons, with electrons orbiting around the nucleus.
• The number of protons defines the element.

Bond Formation by Atoms

• Atoms form bonds to fill their outermost electron shell.
• Number of bonds formed depends on the number of electrons needed to fill or empty the outermost partially filled orbital

Number of Bonds Formed by Bioelements

List of elements and the number of bonds formed by each.

Chemical Bonds

• Types of Chemical Bonds -Intramolecular(covalent and ionic bonds) within a molecule. -Intermolecular (hydrogen bonds, Van der Waals forces, hydrophilic interactions) between molecules.

Relative Chemical Bond Strengths

• Intramolecular bonds require more energy to form but also release more energy when broken compared to intermolecular ones.

Covalent Bonds

• Sharing of electrons between atoms resulting in stable bonds.

Ionic Bonds

• Transfer of electrons between atoms resulting in oppositely charged ions that attract each other.

Hydrogen Bonds

• Attraction between hydrogen and another highly electronegative atom.

Van der Waals Forces

• Temporary electrostatic attraction between molecules.

Electronegativity and Polarity

• Electronegativity is the ability of an atom to attract electrons.
• Polarity arises from unequal sharing of electrons.
• Bond polarity is determined by the difference in electronegativity.

Polar Bonds vs Polar Molecules

• A polar bond is within a molecule.
• Polar molecules involve multiple polar bonds and the overall shape of the molecule.

Water Properties

• Water is a polar molecule.
• Oxygen has a partial negative charge, and hydrogen atoms have partial positive charges.

Importance of Polarity in Solubility

• Polar substances dissolve in polar solvents, and nonpolar substances dissolve in nonpolar solvents.

Acids and Bases

• Acids are proton donors.
• Bases are proton acceptors.

Isomers

• Isomers have the same molecular formula but different atomic arrangements.

Structural Isomers

• Different bonding arrangements between atoms.

Spatial Isomers

• Same bonding arrangement, but different spatial positioning of atoms.

Energy in Biochemistry

• Energy is transferred between molecules in chemical reactions.
• Change in enthalpy measures the heat change in reactions (delta H).
• Exergonic reactions release energy (delta H negative).
• Endergonic reactions require energy input (delta H positive).

Negative delta H - Exothermic

Loss of heat, energy released, Final product temp less than initial reactant temp

Positive delta H - Endothermic

Gain of heat , energy absorbed, Final product temp more than initial reactant temp

Negative Delta G - Spontaneous Reaction

• The reaction will proceed spontaneously.

Spontaneous Reactions:

Reactions occur naturally without external influence

What else determines if a reaction is possible?

Entropy and second law of thermodynamics factors.

Entropy

• Measure of disorder or randomness in a system.
• Higher entropy means more disorder.
• Reactions tend toward higher entropy.

Gibbs Free Energy

• Combines enthalpy and entropy changes.

Exergonic vs Endergonic Reactions

Exergonic reactions release energy; Endergonic reactions require energy.

Conditions Favouring Exergonic Reactions

• Reactions that lose heat and gain entropy are energetically favorable

DeltaG vs DeltaG°

• delta G is the actual free energy change under specific conditions.
• DeltaG° is under standard conditions (298k, 1atm, 1M concentration)

Energy in Food - Gross Energy

• Gross energy is the total energy in food.
• Energy is released by combustion or oxidation.

Useable Energy

Energy for organismic functions such as growth, maintenance, and reproduction

Energy Out

Expenditures over 24hrs, including Basal Metabolic Rate (BMR) and Thermic Effect of Food (TEF), and activity level.

3 factors affecting Obesity Epidemics

Intake of fast food, added sugar, and large portion sizes.

Amino Acids

Building blocks of protein, with 20 standard amino acids, some essential in the diet.

Protein Peptides

• Amino acids linked by peptide bonds into chains, from dipeptides to oligopeptides (short chains) to larger polypeptides that constitute proteins.

Protein Polymers

Polypeptides that are larger (more than 50 aa)

Biological Proteins

Proteins (hundreds to thousands of amino acids) function in various biological roles, in different, complex structures

Protein Structure Levels

Levels of protein structure include primary, secondary, tertiary, and quaternary structures

Structure of Proteins (Detail)

Describes polypeptide sequence order, interactions amongst amino acids for secondary structures (alpha helices, beta sheets), 3D folding for tertiary structures, and interactions of multiple polypeptide subunits in quaternary structures. Includes different forces holding structures together (hydrogen bonds, disulfide bonds etc)

Dynamic vs Static Proteins

• Dynamic proteins are not fixed in one spot in the body. Ex: transporter proteins, enzymes
• Static proteins are fixed to one location in the body. Ex: collagen, actin/myosin

Serum Albumins

• Water-soluble proteins (60% of plasma proteins).
• Maintain osmotic pressure.

Globulins

• Water-soluble proteins (40% of plasma proteins).
• Transport, binding, and eliminating foreign particles

Hemoglobin

• Protein in red blood cells.
• Transports oxygen.

Myoglobin

• Protein in muscle cells.
• Stores oxygen.

Insulin

• Hormone controlling blood glucose levels.

Thyroid Hormones (T3 and T4).

• Produced in thyroid gland.
• Regulate metabolism and growth.

Somatotropin

• Growth hormone produced in the pituitary gland.
• Stimulates growth and development

Collagen

• Structural protein in connective tissues.
• Abundant in mammals.

Elastin

• Flexible protein in connective tissues (skin, ligaments, blood vessels.

Proteoglycans

• Proteins with carbohydrate chains.
• Important components of connective tissues.

Fibronectin

Extracellular matrix protein.

Actin and Myosin

Proteins involved in muscle contraction

Dietary Protein

• Dietary protein intake: 10-35%.
• Essential AA synthesis by body: 10-12.