Ch 2 Chemistry - Chemistry of Life
Chemistry of Life (Saladin Chapter 2) Study Notes
The Atom
Definition of Atom: The simplest unit of matter.
Composed of subatomic particles.
Main three subatomic particles: Proton (), Neutron (), and Electron ().
Definition of Element: The simplest form of matter that possesses unique chemical properties.
Identified by its atomic number, which equals the number of protons.
Elements are listed by atomic number on the periodic table.
Basic Structure of an Atom:
Nucleus: Located at the center, containing protons and neutrons.
Protons and neutrons each have a mass of approximately Atomic Mass Unit (AMU).
Electrons: Orbit the nucleus in a "cloud" or energy shells.
They are very small in mass but possess high energy.
Crucially, electrons determine an atom's chemical binding properties and how atoms interact.
Important Elements in Human Physiology:
Oxygen (O)
Carbon (C)
Hydrogen (H)
Nitrogen (N)
Calcium (Ca)
Phosphorus (P)
Sulfur (S)
Potassium (K)
Sodium (Na)
Chlorine (Cl)
Magnesium (Mg)
Iron (Fe)
Definition of Atomic Weight: The sum of the number of protons and neutrons in an atom's nucleus.
Definition of Isotope: Atoms of the same element (meaning they have the same number of protons) but possess different masses due to a different number of neutrons.
They act chemically the same.
Examples:
Hydrogen: (1 proton, 0 neutrons), (1 proton, 1 neutron), (1 proton, 2 neutrons).
Carbon: All carbon isotopes have an atomic number of (6 protons).
has neutrons.
has neutrons.
has neutrons.
Radioisotope: Isotopes that decay over time, releasing radiation.
Half-life: The time required for half of the radioactive material to decay.
Radiation intensity decreases by half with each half-life interval.
Electrons in Energy Shells привлечение:
Electrons move through specific energy shell areas in space.
Valence electrons: Electrons in the outermost energy shell.
If the valence shell is full, the atom is nonreactive (stable).
If the valence shell is not full, the atom is reactive and will share, gain, or lose electrons to achieve a full, stable shell.
Definition of Ion: A charged atom.
Cation: An atom that loses an electron, resulting in a positive charge (e.g., + ).
Anion: An atom that gains an electron, resulting in a negative charge (e.g., ).
Definition of Electrolyte: Substances that ionize (dissociate into ions) when dissolved in water.
Includes acids, bases, and salts.
Their solutions can conduct electricity.
Physiological Importance: Essential for muscle and nerve cell function, as these cells change charge as electrolytes (e.g.,, ) move across their membranes.
Maintaining electrolyte balance is critical for homeostasis; imbalances can lead to death.
Chemical Bonds, Water, and Solubility
Definition of Molecule: A chemical particle consisting of two or more atoms united by chemical bonds.
Formed by the interaction between electrons of different atoms.
Definition of Compound: A molecule composed of two or more different elements.
Molecular Formula: Represents the elements present by their symbols and the number of atoms of each element as a subscript (e.g., for methane).
A preceding number indicates the number of molecules (e.g., represents two water molecules).
Molecular Weight: The sum of the individual atomic weights of all atoms in a molecule (e.g., C is AMU, H is AMU; so is AMU).
Definition of Isomer: Molecules with the same chemical formula but different shapes (structural arrangements).
The shape significantly affects their chemical interactions (e.g., ethanol and dimethyl ether both have , but different structures and properties).
Chemical Bonds
Covalent Bond: Atoms share electrons to fill their valence shells.
Single covalent bond: Shares one pair of electrons.
Double covalent bond: Shares two pairs of electrons.
Represented by a solid line in diagrams.
Nonpolar Covalent Bond: Electrons are shared equally between atoms.
Electrons spend approximately equal time around each nucleus due to equal attraction.
Typically occurs between atoms of the same element (e.g., C-C, O=O) or between Carbon and Hydrogen (C-H).
These are strong bonds.
Polar Covalent Bond: Electrons are shared unequally between atoms.
Electrons are more strongly attracted to one atom, spending more time around its nucleus.
Results in slight partial charges: one atom gets a slight negative charge () and the other a slight positive charge () (e.g., O-H bond in water, where Oxygen is and Hydrogen is ).
Water () is an example of a molecule with polar covalent bonds internally.
Ionic Bond: An attraction between oppositely charged ions (cation and anion).
Weaker than covalent bonds; forms easily but can separate in water.
Example: Sodium chloride (NaCl) forms an ionic bond, but readily dissociates into and in water.
Hydrogen Bond: A weak attraction between a slightly positive hydrogen atom (which is already part of a polar covalent bond) and a slightly negative oxygen or nitrogen atom of another molecule or a different region of the same molecule.
Represented by dots or a broken line.
Crucial for interactions between water molecules.
Stabilizes the three-dimensional structures of large molecules like proteins and DNA.
Van der Waals Forces: Very weak, brief attractions between neutral atoms.
Occur due to momentary, fleeting shifts in electron distribution, creating temporary opposite charges.
Important in lipid interactions and the structure of cell membranes.
Water and Solutions
Water as a Polar Molecule:
Its bent, triangular shape (with negative charge concentrated near oxygen and positive charges near hydrogen atoms) results from its polar covalent O-H bonds.
This polarity is fundamental to water's unique properties.
Hydrocarbons (Nonpolar):
Molecules composed only of hydrogen and carbon (e.g., ).
Electrons are shared equally, making them nonpolar.
They do not interact with water (hydrophobic).
Properties of Water (due to hydrogen bonds):
Solvency: Water is often called the "universal solvent" because its polarity allows it to dissolve other polar chemicals and charged particles.
This property supports nearly all metabolic reactions.
Hydrophilic substances: Substances that dissolve in water; they are typically polar or charged (e.g., salts, sugars). "Opposite charges attract" principle.
Hydrophobic substances: Nonpolar substances that do not dissolve in water (e.g., lipids, oils).
Hydration Sphere: Water molecules surround ions (charged particles), with the oxygen (slight negative) orienting towards positive ions and hydrogen (slight positive) orienting towards negative ions.
Cohesion: Water molecules "stick to water molecules" (molecules of the same substance cling together).
Caused by hydrogen bonds between the slight opposite charges of adjacent water molecules.
Surface tension: The resistance of water's surface to being broken, a result of cohesion (e.g., belly flop).
Adhesion: Water molecules are attracted to other polar particles.
Occurs due to opposite charges between water and a different substance.
Important for creating films at body tissue membranes (e.g., between pericardial layers).
Chemical Reactivity: Water is directly involved in many metabolic reactions.
It can ionize into and ions.
Water is used to build (dehydration synthesis) and break (hydrolysis) molecular bonds.
Thermal Stability:
High Heat Capacity: Water can absorb a significant amount of energy without a large change in temperature due to hydrogen bonds needing to be broken before temperature increases.
Can release stored energy to cool the body (e.g., sweat evaporation: liquid water turns to vapor, carrying heat away).
Temperature reflects molecular motion; cooler means less motion, warmer means more motion.
Mixtures
Mixture: Substances that are physically blended but not chemically combined.
Solution:
Particles are very small (under ).
Typically transparent.
Can pass through membranes.
Do not separate on standing.
Consists of a solvent (more abundant, often water) and a solute (dissolved in the solvent).
Example: Kool-Aid.
Colloid:
Particles range from to .
Scatter light, appearing cloudy.
Cannot pass through membranes.
Remain mixed on standing.
Can often convert between liquid and gel states (e.g., cytoplasm, extracellular fluid, milk proteins).
Example: Albumin protein in blood.
Suspension:
Particles are large (>100 \text{ nm}).
Appear cloudy to opaque.
Cannot penetrate membranes.
Separate upon standing.
Example: Cells in blood.
Emulsion: One liquid is suspended within another liquid.
Example: Oil and vinegar, fat in breast milk (oil-in-water emulsion).
Concentration
Concentration: How much solute is present in a given volume of solution.
Weight per volume: Expressed as units like mg/dL (milligrams per deciliter).
Molarity (M): Represents the number of solute atoms/molecules per volume.
atoms/molecules (Avogadro's number).
solution contains of solute in of solution.
Millimolar () is a common unit in physiology.
Molarity is more useful in physiology as it accounts for the number of particles, not just their mass.
Milliequivalents per liter (mEq/L): Used for electrolytes, taking into account both the number of ions and their charge.
Crucial for muscle and nerve function.
pH
Definition of pH: The negative logarithm of the hydrogen ion () concentration.
Expressed as . To find pH, take the exponent of the concentration when written in scientific notation (e.g., has a pH of ).
Hydrogen ion (): Also known as a proton.
Ionization of Water: Water naturally ionizes to a small extent into and ().
Definition of Acid: A proton () donor.
Example: Carbonic acid () releases ().
Definition of Base: A proton () acceptor.
Examples:
Bicarbonate () accepts ().
Ammonia () accepts ().
Hydroxide () accepts (e.g., from NaOH).
The pH Scale: Ranges from to .
Acidic: pH below (e.g., pH ; pH ).
Indicates a higher concentration of than ions.
Lower pH values indicate stronger acidity.
Neutral: pH of .
Indicates an equal concentration of and ions (e.g., pure water has and ).
Basic (Alkaline): pH above (e.g., pH ; pH ).
Indicates a higher concentration of than ions.
Higher pH values indicate stronger basicity.
The pH scale is inverse (higher means lower pH) and exponential (a change of pH unit represents a tenfold change in concentration).
Definition of Buffer: Chemical systems that resist drastic changes in pH.
Mechanism:
If pH is too low (acidic), the buffer system accepts excess ions (e.g., bicarbonate accepts to form carbonic acid).
If pH is too high (basic), the buffer system releases ions (e.g., carbonic acid dissociates to release ).
Buffers are essential for maintaining pH within a narrow range, crucial for homeostasis and survival.
Chemical Reactions and Energy Transfer
Energy: The capacity to do work (e.g., move something, break or build chemical bonds).
In the body, glucose and other molecules are broken down to release energy.
This energy is stored in adenosine triphosphate (ATP) molecules.
ATP is then used to power cellular work.
Chemical Reaction: A process where covalent or ionic bonds are formed or broken.
Represented by a chemical equation:
Reactants: Substances present at the start of the reaction.
Products: Substances produced at the end of the reaction.
An arrow indicates the direction of the reaction.
Decomposition Reaction (Catabolic): Breaks down a larger molecule into smaller ones.
Typically releases energy.
Glucose Oxidation: A primary example where glucose is broken down to release energy.
Hydrolysis: A specific type of decomposition reaction where water is used to break a covalent bond.
A water molecule () is added, with going to one piece of the broken molecule and going to the other.
Synthesis Reaction (Anabolic): Joins smaller molecules to form a larger one.
Typically requires energy input.
Dehydration Synthesis: A specific type of synthesis reaction where water is removed to form a covalent bond.
One molecule releases and another releases , which combine to form water, linking the two molecules.
Oxidation / Reduction (Redox Reactions): Involve the transfer of electrons between atoms, which is critical for energy transfer in human cells.
Electrons = Energy: The movement of electrons often means the movement of energy. Electrons can also move as part of hydrogen atoms.
LEO / OIL (Lose Electrons Oxidation): An atom that loses electrons is said to be oxidized.
The oxidized atom has fewer electrons and thus less energy.
GER / RIG (Gain Electrons Reduction): An atom that gains electrons is said to be reduced.
The reduced atom has more electrons and thus more energy.
Example: Cellular respiration ():
Glucose () is oxidized: It starts in a reduced state (has many hydrogen atoms/electrons) and loses hydrogen/electrons to become carbon dioxide ().
Oxygen () is reduced: It starts in an oxidized state (lacks hydrogen/electrons) and gains hydrogen/electrons to become water ().
Organic Chemistry and Biomolecules
Organic Compounds: Compounds primarily based on carbon.
Carbon Backbone: Carbon atoms form stable, nonpolar covalent bonds with other carbon atoms (C-C-C chains).
Importance of Carbon: Carbon has four available valence bonds, allowing it to easily bind with other carbon atoms and many other elements, forming diverse and complex molecular structures.
Functional Groups: Specific clusters of atoms that attach to carbon backbones, determining the molecule's chemical properties.
Hydroxyl ()
Methyl ()
Carboxyl ()
Amine ()
Phosphate ()
Four Major Biomolecules (Macromolecules):
Carbohydrates
Lipids
Proteins
Nucleic acids
Monomers and Polymers:
Monomer: A small, single subunit.
Polymer: A large molecule formed by joining many identical or similar monomers through covalent bonds.
Formation: Polymers are built from monomers via dehydration synthesis (water removed).
Breakdown: Polymers are broken down into monomers via hydrolysis (water added).
Key relationships:
Simple sugar is the monomer for Carbohydrate.
Fatty acid (kinda) is the monomer for Lipid (kinda).
Amino acid is the monomer for Protein.
Nucleotide is the monomer for Nucleic acid.
Carbohydrates
Structure: Typically have the formula . They are hydrophilic due to the presence of many oxygen atoms.
Monomer: Monosaccharide (Simple Sugar):
Hexose Sugars (6 carbons): Glucose, Galactose, Fructose. These are isomers, all having the chemical formula .
Pentose Sugars (5 carbons): Ribose (found in RNA) and Deoxyribose (found in DNA).
Disaccharide: Formed by the dehydration synthesis of two monosaccharides.
Sucrose (table sugar): Glucose + Fructose.
Lactose (milk sugar): Glucose + Galactose.
Oligosaccharides: Chains of a few sugars (e.g., on the outside of cell membranes).
Glycolipids and Glycoproteins: Serve as cell identification markers.
Polysaccharides (Many Sugars):
Glycogen: The primary glucose storage polysaccharide in humans.
Stored in the liver and muscles.
Built when blood glucose is high (after eating) and broken down to release glucose when blood glucose levels fall (between meals).
Starch: Plant glucose storage polysaccharide.
Synthesized by plants via photosynthesis.
Humans digest starch to absorb glucose.
Cellulose: Provides strength to plant cell walls.
Humans lack the enzymes to digest cellulose; it functions as dietary fiber, aiding in the movement of contents through the large intestine.
**Carbohydrate Functions:
Quick Energy Source: Easily converted to glucose, which is then oxidized in mitochondria during aerobic cell respiration to produce a large amount of ATP.
Conjugated Carbohydrates: Join with other molecules to form larger structures.
Glycolipids and Glycoproteins: Act as cell surface identification markers.
Mucus: A sticky lubricant.
Proteoglycans: Involved in cell adhesion, lubrication, and filling spaces in cartilage and other tissues.
Lipids
Structure: Primarily composed of carbon and hydrogen, making them largely hydrophobic. Contain a small amount of oxygen, typically in carboxyl (COOH) groups.
Not considered true macromolecules because they are not typically large polymers of repeating monomers in the same way as carbohydrates or proteins.
Fatty Acid (Monomer-like Unit):
A chain of to carbons with a carboxyl group (COOH) at one end.
Saturated Fatty Acid: Contains only single C-C bonds; the carbon chain is straight.
Typically solid at room temperature (e.g., animal fats).
Unsaturated Fatty Acid: Contains one or more C=C double bonds; the carbon chain has "bends" or kinks.
Typically liquid (oils) at room temperature (e.g., plant oils).
Essential Fatty Acids (EFAs): Fatty acids that the human body cannot synthesize and must be obtained from the diet (e.g., linoleic acid (Omega-6 EFA), alpha-linolenic acid (Omega-3 EFA)).
Triglyceride (Neutral Fat - Polymer-like):
Formed by the dehydration synthesis of a glycerol molecule (a 3-carbon carbohydrate backbone) with three fatty acids.
water molecules are removed (one OH from glycerol and one H from each fatty acid combine to form ).
A covalent bond is formed between glycerol and each fatty acid.
Functions:
Primary form of energy storage in the body.
Provides thermal insulation.
Acts as a shock absorber for organs.
Forms adipose tissue.
Phospholipids:
Composed of a glycerol backbone, two fatty acid tails (hydrophobic), and a phosphate group (and often other functional groups) forming a hydrophilic head.
The two fatty acid tails can be saturated (straight) or unsaturated (bent).
Amphipathic: Possesses both hydrophilic and hydrophobic regions.
Function: Major component of cell membranes, forming the phospholipid bilayer.
The hydrophobic tails face inwards, creating a barrier to polar and charged particles.
The hydrophilic heads face outwards, interacting with water in the extracellular fluid and cytoplasm.
Eicosanoids: Lipid compounds that act as cell signaling molecules.
Examples: Prostaglandins, leukotrienes, thromboxanes, lipoxins.
Steroids (Sterols): Lipids characterized by a distinctive structure of carbons arranged in four rings.
Derived from cholesterol.
of cholesterol comes from animal food, while is synthesized by the human body.
Functions of Cholesterol: Stabilizes animal cell membranes, crucial for nervous system function, precursor for other steroids.
Functions of Steroids: Include hormones (e.g., sex hormones, cortisol) and bile acids (aid in fat digestion).
Summary of Lipid Functions:
Bile acids: Steroids aiding fat digestion and nutrient absorption.
Cholesterol: Cell membrane component; precursor for other steroids.
Eicosanoids: Chemical messengers between cells.
Fat-soluble vitamins (A, D, E, K): Involved in various functions like blood clotting, wound healing, vision, calcium absorption.
Fatty acids: Precursor of triglycerides; source of energy.
Phospholipids: Major component of cell membranes; aid in fat digestion.
Steroid hormones: Chemical messengers between cells.
Triglycerides: Energy storage; thermal insulation; filling space; binding organs; cushioning organs.
Proteins
Monomer: Amino Acids:
Each amino acid has a central carbon atom bonded to:
An amine group ()
A carboxyl group ()
A hydrogen atom ()
A unique "R" group (radical group or side chain) that varies among the different amino acids.
R Group Characteristics:
Polar R group: Contains oxygen or nitrogen.
Nonpolar R group: Contains mostly carbon and hydrogen.
Cysteine: Contains sulfur (S), allowing for covalent disulfide bonds.
Amino Acids as Neurotransmitters: Some amino acids or their derivatives function as neurotransmitters (e.g., pathways for tyrosine to dopamine/norepinephrine, or tryptophan to serotonin).
Peptide Bond: A covalent bond that joins amino acids.
Formed by dehydration synthesis: The incoming amine group () of one amino acid joins the existing carboxyl group () of another.
A molecule of water is removed.
Oligopeptides and Polypeptides:
Dipeptide: amino acids.
Tripeptide: amino acids.
Oligopeptide: A few amino acids (typically to or less).
Polypeptide: Many amino acids (more than ).
Protein: A molecule consisting of amino acids, folded into a specific three-dimensional (3D) shape (conformation).
Protein Structure (4 Levels): The specific 3D shape is critical for protein function, resulting from various chemical interactions.
Primary Structure: The unique linear sequence (order) of amino acids in the polypeptide chain.
Secondary Structure: Localized, repetitive folding patterns formed by hydrogen bonds between the hydrogen of one amino acid's amine group and the oxygen of another amino acid's carboxyl group along the backbone.
Alpha helix: A spiral or coil shape.
Beta sheet: A pleated, zig-zagged shape.
Tertiary Structure: The overall three-dimensional bending and folding of the polypeptide chain, beyond the secondary structures.
Results in either a globular (compact, blob-like) or fibrous (long, thread-like) shape.
Driven by interactions such as: hydrophobic interactions (nonpolar groups cluster inward), hydrophilic interactions (polar groups face outward), Van der Waals forces, ionic interactions, and covalent disulfide bridges (formed between two cysteine side chains, stabilizing the structure).
Quaternary Structure: Present in proteins composed of two or more separate polypeptide chains (subunits).
Example: Hemoglobin protein has four polypeptide chains.
Formed by noncovalent interactions between the different polypeptide subunits.
These interactions influence each other's shape and function.
Protein Conformation (Shape Flexibility):
Proteins can undergo reversible changes in their three-dimensional shape, which is essential for their function.
Receptor proteins: Located at the cell surface, they change shape when a specific chemical (ligand) binds to them, initiating changes inside the cell.
Enzyme proteins: Flex their shape to become more efficient catalysts.
Enzymes (Protein Catalysts):
Are proteins that act as biological catalysts, speeding up specific chemical reactions without being permanently changed themselves.
Mechanism of Action:
Specificity: Each enzyme is highly specific for its substrate (reactant) due to complementary shapes.
The substrate binds to a specific region on the enzyme called the active site, forming an enzyme-substrate complex.
The enzyme stresses the chemical bonds of the substrate, holds it in the optimal position, and attracts atoms, which lowers the activation energy required for the reaction.
This significantly speeds up the reaction.
Once products are formed, they no longer fit the active site and are released.
Activation Energy: The initial energy investment required to get a chemical reaction to start, even if the reactants' bonds are unstable.
Denaturation: The process by which a protein unfolds from its specific 3D shape, rendering it nonfunctional.
Caused by extreme environmental conditions (e.g., high temperature, extreme pH).
Disrupts hydrogen bonds and other chemical interactions that stabilize the protein's conformation.
Sometimes reversible, aided by chaperone proteins.
Irreversible denaturation leads to permanent loss of function.
Effect of Temperature and pH on Enzyme Activity:
Each enzyme has an optimal temperature and pH range at which it maintains its proper shape and functions most efficiently.
Deviations from this optimal range can cause the protein to denature, leading to a loss of function.
Protein Functions:
Structure: Provide physical support and strength (e.g., keratin in skin).
Communication: Act as hormones or receptors that bind ligands, transducing signals.
Membrane Transport: Form channels to regulate passage of polar substances in and out of cells, or act as carriers to transport substances across membranes (important for muscle and nerve cell activity).
Catalysis: Enzymes accelerate chemical reactions.
Recognition & Protection: Include glycoproteins for immune system recognition, antibodies that tag foreign substances, and blood clotting proteins.
Movement: Proteins change shape to facilitate movement (e.g., molecular motors, muscle contraction).
Cell Adhesion: Bind cells together to form tissues, important for processes like sperm joining an egg or immune cells grabbing foreign invaders.
Nucleic Acids
Monomer: Nucleotide:
Composed of three parts:
A pentose (5-carbon) sugar.
A nitrogenous base.
One or more phosphate groups.
ATP (Adenosine Triphosphate): A functionally relevant nucleotide that serves as the primary "energy currency" of the cell.
Composed of a ribose sugar, adenine (a nitrogenous base), and three phosphate groups.
Stores high energy in the bond between its second and third phosphate groups.
Energy is released for cellular work when this bond is broken, converting ATP (high energy) to ADP (adenosine diphosphate, low energy) and an inorganic phosphate ().
Energy from the breakdown of glucose etc. is used to convert ADP + back to ATP.
Kinase enzymes: Enzymes that add phosphate groups (phosphorylate) to molecules.
Nucleic Acids (Polymers): Polymers of nucleotides.
Built via dehydration synthesis and broken down via hydrolysis.
The two main types are DNA and RNA.
Information Flow: The central dogma of molecular biology describes the flow of genetic information: DNA contains the instructions, which are transcribed into RNA, and then translated into Protein.
DNA (Deoxyribonucleic Acid):
Function: The genetic blueprint that contains all the instructions to make proteins.
Location: Primarily in the nucleus of eukaryotic cells.
Replication: Copies itself and passes one copy to new cells during cell division.
Sugar: Deoxyribose.
Nitrogenous Bases: Adenine (A), Thymine (T), Guanine (G), Cytosine (C).
RNA (Ribonucleic Acid):
Function: Involved in the work of protein synthesis.
Location: Made in the nucleus but functions primarily in the cytoplasm.
Sugar: Ribose.
Nitrogenous Bases: Adenine (A), Uracil (U - replaces thymine), Guanine (G), Cytosine (C).
Three Main Types of RNA:
Messenger RNA (mRNA): Carries a copy of the DNA instructions from the nucleus to the ribosomes in the cytoplasm. It specifies the order of amino acids for protein synthesis.
Ribosomal RNA (rRNA): A structural and catalytic component of ribosomes, where it helps catalyze the formation of peptide bonds between amino acids.
Transfer RNA (tRNA): Brings specific amino acids to the ribosome, matching them to the mRNA sequence.
Overall Process: At the ribosome, amino acids are linked together in the exact order specified by the mRNA, forming a polypeptide chain. This chain then folds into a functional protein.