Chemical Bonds and Water

• Chemical bonds hold atoms together to form molecules and compounds.

Types of Chemical Bonds

• Ionic bonds form through the transfer of electrons between atoms, creating positively charged cations and negatively charged anions that attract each other.
• An example of an ionic bond is NaCl (sodium chloride), where sodium (Na) loses an electron and chlorine (Cl) gains one.
• Covalent bonds, the strongest type, are formed when atoms share electrons to fill their outer shells.
• Non-polar covalent bonds involve equal sharing of electrons, such as in O2 (oxygen).
• Polar covalent bonds involve unequal sharing of electrons, with one atom having a stronger pull, like oxygen in H2O (water).
• Hydrogen bonds are weak bonds between polar molecules, where hydrogen is attracted to electronegative atoms like oxygen or nitrogen, and are crucial in water, protein, and DNA structures.

Water

• The oxygen in our air comes from water, released during photosynthesis.
• Water comprises 60-70% of body weight and fills the space in cells not occupied by organelles.
• A solute is a substance being dissolved, like salt in water, while a solvent is the substance doing the dissolving, like water.
• Hydrophilic molecules interact with water; hydrophobic molecules do not.
• Water is a good solvent, dissolving the most solutes, including food and nutrients.
• Water is a polar covalent molecule involved in biochemical reactions like dehydration synthesis and hydrolysis.
• Dehydration synthesis makes molecules by removing water; hydrolysis splits molecules using water.
• Water ionizes, dissociating into ions, which determines pH.
• As pH increases, hydrogen ion concentration decreases.
• pH influences molecule behavior and bodily functions, especially proteins.
• Buffers, like H₂CO₃ ↔ HCO₃⁻ + H⁺, help maintain stable pH.
• Due to hydrogen bonds, water has a high specific heat, requiring much energy to raise its temperature and helping regulate body and planetary temperatures.
• Evaporative cooling, like sweating, helps cool the body.
• High cohesion means water molecules stick together due to hydrogen bonds, important for blood flow against gravity.

Biomolecules

• Biomolecules are biologically important molecules in living organisms.
• There are 92 naturally occurring elements; more can be synthesized.
• Examples of biomolecules include water, carbohydrates, proteins, lipids, and nucleic acids.
• Organic molecules contain carbon

Carbohydrates

• Organic biomolecules contain carbon, hydrogen, and oxygen, and often end in -ose (e.g., glucose, fructose).
• Carbohydrates are water-soluble and made of sugar monomers with ring structures.
• Monosaccharides are single sugar rings, like glucose (C₆H₁₂O₆); disaccharides consist of two rings, like sucrose; polysaccharides include three or more rings.
• Animals store glucose as glycogen in the liver and muscles for fuel; excess glucose is converted to fat.
• Plants store glucose as starch and use it to build cellulose for cell walls.
• Insects use glucose for chitin in exoskeletons.

Lipids

• Lipids are mostly insoluble in water and include triglycerides (fats), phospholipids, and steroids.
• Triglycerides have one glycerol molecule and three fatty acid chains; COOH (carboxyl group) is an acidic group.
• Saturated fatty acids have no double bonds, monounsaturated have one, and polyunsaturated have two or more.
• Unsaturated fats are typically liquid at room temperature.
• LDLs (low-Density Lipoproteins) deliver lipids to cells.
• Fat is stored in adipose tissue.
• Artificial hydrogenation creates unhealthy trans fats by altering unsaturated fats.
• In cis form, hydrogen atoms are on the same side of the double bond, bending the chain; in trans form, they are on opposite sides, making the chain straighter and more rigid.
• Products with partially hydrogenated oils contain trans fats.
• If a serving contains less than 0.5g of trans fat, it can be listed as 0g on the label.
• Omega-3 fatty acids have the first double bond on the third carbon from the omega end, sourced from fish oils, flaxseeds, and chia seeds, and are generally anti-inflammatory.
• Omega-6 fatty acids have the first double bond on the sixth carbon from the omega end, sourced from vegetable oils, nuts, and seeds, and can be pro-inflammatory in excess.
• Phospholipids have a phosphate group, glycerol, and two fatty acids, acting as plasma membrane components and emulsifiers.
• Steroids are lipids with four fused carbon rings, derived from cholesterol and convertible into hormones.

Proteins

• Proteins include carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur, structured as long chains of amino acid monomers, and are mostly soluble in water.
• Essential amino acids vary across species.
• The R group (side chain) distinguishes one amino acid from another.
• A polypeptide is a long chain of amino acids not yet folded; a protein is a polypeptide folded into a functional 3D structure.
• Primary protein structure is the sequence of amino acids; secondary involves initial folding into alpha helices and beta sheets; tertiary is further folding into a 3D shape; quaternary involves two or more interacting polypeptides.
• A protein's shape determines its function, and denaturation from heat and pH can alter its shape, causing loss of function.
• There are only 20 different amino acids, combined in various sequences to form different proteins.
  • Enzymes catalyze biochemical reactions.
  • Transport molecules across membranes or within cells.
  • Provide structural support.
  • Mediate immune responses.
  • Perform hormonal signaling.

Nucleic Acids

• DNA (Deoxyribonucleic Acid) is a double-stranded helix with bases adenine (A), thymine (T), cytosine (C), and guanine (G), where A pairs with T and C pairs with G, and has deoxyribose sugar.
• RNA (Ribonucleic Acid) is single-stranded with bases adenine (A), uracil (U), cytosine (C), and guanine (G), where A pairs with U and C pairs with G, and has ribose sugar.
• Nucleotides are the building blocks, with a phosphate group, a 5-carbon sugar, and a nitrogenous base.
• DNA contains the genetic code transcribed into mRNA, which is translated into proteins.
• Proteins carry out body functions and require energy.

ATP

• ATP (Adenosine Triphosphate) has a nitrogenous base (adenine), ribose sugar, and three phosphate groups.
• ATP functions in temporary energy storage.
• Energy is stored in the bond between the second and third phosphate groups. - ATP ↔ ADP + Pi + Energy - During Hydrolysis (right) ATP releases energy when broken down into ADP - During Dehydration Synthesis (left) ATP is formed from ADP and Pi, storing energy

Dehydration Synthesis

• Dehydration Synthesis is the process where two molecules are joined together to form a larger molecule, and in the process, a water molecule is removed.
• Key in building larger molecules like proteins and polysaccharides.
• Used when two monosaccharides join to form sucrose.

Mono, Di and Polysaccharides

• Monosaccharides: Simplest sugars and are the building blocks of carbohydrates.
• Example: Glucose or fructose.
• Disaccharides: Made up of two monosaccharides joined together by a dehydration synthesis reaction.
• Example: Sucrose, which is made from glucose and fructose.
• Polysaccharides: Large, complex carbohydrates made up of many monosaccharides linked together.
• Example: Starch or glycogen.

Activation Energy and Catalysts

• Activation Energy: The energy required to start a chemical reaction.
• Think of it needing energy to roll a ball up a hill before it can come down.
• Catalysts: Substances that lower the activation energy required for a reaction to occur.
• Enzymes are the most common catalysts.

Aerobic vs Anaerobic Respiration

• Aerobic Respiration: Occurs with oxygen and produces lots of ATP, carbon dioxide (CO₂), and water (H₂O).
• Anaerobic Respiration: Occurs without oxygen, produces much less ATP, and yields byproducts like lactic acid or ethanol and CO₂.

Chemiosmosis

• Chemiosmosis: Protons (H⁺) are pumped across the mitochondrial membrane, creating a proton gradient.
• Protons flow back through ATP synthase, producing ATP from ADP and phosphate.
• Chemiosmosis: How cells make the majority of ATP during cellular respiration

Cell Theory

• All living things are composed of cells.
• A cell is the smallest unit of life.
• All cells arise from pre-existing cells.

Characteristics of All Cells

• Reproduction: Cells must be capable of cell division.
• Cell Material: Cells require the production of new cell materials for growth or repair.
• Energy: Energy is required to make cells and to maintain cellular activities.
• Structures: All cells have a plasma membrane (outer boundary) and cytoplasm (internal fluid, including cytosol).
• Cytosol: The fluid inside the cell, excluding organelles and other structures.
• Chemical reactions, such as dehydration synthesis (building molecules) and hydrolysis (breaking down molecules), are involved in energy conversion.

Cell Size

• The size of a cell is limited by the surface area-to-volume ratio.
• As the cell grows larger, its volume increases faster than its surface area, making it harder for the cell to exchange materials.
• To maximize efficiency, a cell's plasma membrane needs a large surface area relative to its internal volume.

Prokaryotic Cells

• Examples: Bacteria (including archaea)
• Characteristics:
• Have a plasma membrane.
• No membrane-bound organelles.
• Have DNA but it is not enclosed in a nucleus; the DNA is found in the nucleoid region.
• Typically smaller and simpler in structure.

Eukaryotic Cells

• Examples: Plants, animals, protists, fungi
• Characteristics:
• Have a plasma membrane.
• Contain many membrane-bound organelles.
• Have a nucleus that contains the cell’s DNA.
• Typically larger and more complex than prokaryotic cells.

Plasma Membrane

• Controls what gets in and out of the cell.
• Composed of phospholipids arranged in a bilayer.
• Behaves like a fluid with lipids and proteins moving laterally (fluid mosaic model).
• Cholesterol maintains membrane fluidity and stability.
• Integral proteins span the membrane, involved in transport and signal transduction.
• Peripheral proteins are located on the membrane surface, involved in signaling and recognition.
• Proteins transport molecules, catalyze reactions, act as receptors, recognize cells, and allow cell adhesion.

Transport Mechanisms

• Passive Transport (No energy required):
  • Diffusion: High to low concentration. - Simple Diffusion: Moves directly through the lipid bilayer. - Facilitated Diffusion: Protein channels that allows molecules to move easier. - Osmosis: Water diffusion. - Hypertonic solution: Water moves out of the cell. - Isotonic solution: No net water movement. - Hypotonic solution: Water moves into the cell.
    • Active Transport (Requires energy):
      • Moves substances against their concentration gradient. - Example: Na+/K+ pump: Pumps 3 sodium ions out of the cell and 2 potassium ions into the cell.

Vesicle Transport (Bulk Transport)

  - Exocytosis: Transport of material OUT of the cell
  - Endocytosis: Transportation of material IN to the cell
        - Phagocytosis: Cell Eating
        - Pinocytosis: Cell drinking
       - Receptor-mediated endocytosis: molecules bind to specific receptors triggering vesicle formation and internalization.

Internal Cell Structure

• Nucleus: Contains DNA, surrounded by a double membrane (nuclear envelope) with pores, and houses the nucleolus for ribosome synthesis.
• Ribosomes: Synthesize proteins, found in the cytosol or on the rough ER.
• Endoplasmic Reticulum (ER):A network of membranes that form cisternae, involved in protein and lipid synthesis. - Rough ER: Studded with ribosomes; responsible for protein folding and transport. - Smooth ER: Lacks ribosomes; involved in lipid synthesis and detoxification.
• Golgi Apparatus: Modifies and packages proteins, then ships them in vesicles.
• Peroxisomes: Break down fatty acids and detoxify substances.
• Lysosomes: Break down old organelles and cellular debris, sometimes causing cell death (autolysis). - Lysosomal Storage Disease (LSD): - Tay-Sachs disease: A type of lysosomal storage disease that affects the nervous system due to a genetic mutation that causes a lack of an enzyme leading to accumulation of lipids in the brain and nerve cells.
• Mitochondria: Produce ATP, with smooth outer membrane, and a highly folded inner membrane (cristae).

Cytoskeleton

• Maintains cell shape and anchors organelles.
• Dynamic structure, changing as needed and made of protein filaments.
  • Microtubules: Made of tubulin (thickest filaments).
  • Microfilaments: Made of actin (used in muscle contraction).
  • Intermediate filaments: Vary in structure (defective in ALS).
• Cilia and Flagella: Made of microtubules in a 9+2 pattern. - Cilia is short and numerous, like found in lining of the respiratory tract. - Flagella longer, with a motility function.

Cell Metabolism

• Catabolism: Breaks down molecules (e.g., glucose breakdown).
• Anabolism: Builds larger molecules (e.g., protein synthesis).
• Enzymes: Catalyze cell reactions.
• 1st Law of Thermodynamics: Energy is neither destroyed, but it can change form.
• 2nd Law of Thermodynamics: Energy transformations result in a loss of heat, leading to inefficiencies.

Types of Reactions

• Endergonic reactions: Require an energy input.
• Exergonic reactions: Release energy.
• Activation Energy: The energy required to begin any reaction.
• Catalysts: Activate the reaction without energy.

Substrate

• Substrate: Is the molecule that the enzyme works on.
• Active Site: The part of the enzyme that binds to the substrate.
• Suffix: -ase (e.g., trypsin, pepsin, lysozyme).
• Prefix: Named for the substrate they act on (e.g., sucrase breaks down sucrose, proteases break down proteins)

ATP and Cellular Respiration

• Fuels the process with Glucose molecule
• Efficiency in using glucose is roughly 30-40%

Types of Cellular Respiration

• Aerobic Respiration: Requires oxygen to occur. - Yields up to 30 ATP (large amount)
• Anaerobic Respiration: Does not require oxygen to occur - 2 steps: Glycolysis and Fermentation - End Product Lactic Acid.

Cellular Respiration

• Glycolysis: Occurs in the cytosol, converting 1 glucose into 2 molecules of pyruvic acid.
  • The product of this reaction is 2 ATP.
• Occurs with 2 phases: Energy Investment or Energy Harvest
• Conversion to Acetyl CoA: occurs in the mitochondria, where 2 pyruvates is converted into 2 Acetyl CoA
• Kreb's Cycle: Final destination is Mitochondria and produces roughly 2 ATP
• Electron Transport Chain: Occurs in the mitochondria.
  • Produces 28 ATP per glucose molecule. -Chemiosmosis
  • Occurs from the electron transport chain.
  • Protons move down their concentration gradient through the inner mitochondrial membrane
  • Occurs through membrane protein ATP synthase.
    • Results in the release of energy, creating ATP.
• End of the Cycle
  • Oxygen accepts the low level energy from the process and forms the molecule water.

DNA

• Made of nucleotides
  • Phosphate -Sugar
  • Base
• It contains two strands of nucleotides that are connected by hydrogen bonds.
• Helicase: Is the enzyme that unwinds the strand and breaks the bonds.
• Each strand is used as a template of a new one to form as a result.
• DNA Polymerase: Adds new strands to the template in the DNA in the form of nucleotides.
• Mistakes can form, but repair enzymes attempt to stop them.

RNA

• Bases used: Adenine (A), Uracil (U), Cytosine (C), Guanine (G)
  • U is replacing "T" from DNA
• 3 types of RNA -mRNA: Is the messenger, carrying the genetic information from the DNA -rRNA: Combine with the proteins to form ribosomes -tRNA: Delivers amino acids

Genes

• Dictates the production of proteins.
• A strand may contain 100's to thousands of different genes.
• DNA transcribed into mRNA which is translated into polypeptides in the cytoplasm.