Chemistry of Living Things Lecture Review
Chapter 2: Chemistry of Living Things
Chemistry Fundamentals
Chemistry: The study of matter and energy.
Matter:
Anything that has mass and occupies space.
Composed of elements.
Energy: The power to do work.
Elements:
Pure form of matter that cannot be broken down.
Listed on the Periodic Table of Elements, which shows all known elements in order of increasing atomic number.
Example: Sodium (Na), Chlorine (Cl), which combine to form Sodium Chloride (NaCl).
Atoms and Subatomic Particles
Atoms: Composed of subatomic particles.
Subatomic Particles:
Protons: Positively charged particles found in the nucleus.
Neutrons: Neutrally charged particles found in the nucleus.
Electrons: Negatively charged particles orbiting the nucleus in shells.
Atomic Number: The number of protons in an atom's nucleus. It determines the element.
Mass Number: The sum of protons plus neutrons in the nucleus.
Atoms of the various elements differ in the number of subatomic particles.
Isotopes:
Atoms of the same element (same number of protons) that have a different number of neutrons.
This results in a different atomic mass.
Radioisotopes: Unstable isotopes that give off radiation.
Uses of Radioisotopes:
Dating fossils (e.g., carbon-14 (^{14}C)).
Diagnostic imaging in medicine.
Cancer treatment.
Power supply for implants such as cardiac pacemakers.
Free Radicals:
Atoms with unpaired electrons, making them highly reactive.
Can damage proteins and DNA.
Can speed up cellular aging.
Most stable atoms have all shells filled and all electrons paired.
Molecules and Energy
Molecule: A stable association between two or more atoms.
Can be two or more of the same kind of atoms (e.g., Oxygen (O_2)).
Can be different kinds of atoms (e.g., Water (H_2O), Table salt (NaCl)).
Energy Fuels Life's Activities:
Energy: The capacity to do work.
Potential Energy: Stored energy.
Kinetic Energy: Energy in motion, doing work.
Potential energy can be transformed into kinetic energy.
Electron Potential Energy:
Electrons possess potential energy.
Each electron shell has a specific level of potential energy.
Shells farther from the nucleus contain electrons with more potential energy. This is analogous to a ball bouncing down a flight of stairs: higher steps have more potential energy.
Chemical Bonds
Chemical Bonds: Attractive forces holding atoms together.
Three Main Types of Chemical Bonds:
Covalent Bonds:
Formed by the sharing of a pair of valence electrons between two atoms.
The shared electrons count as part of each atom's valence shell.
A molecule consists of two or more atoms held together by covalent bonds.
Single Covalent Bond: Sharing of one pair of valence electrons.
Double Covalent Bond: Sharing of two pairs of valence electrons.
Non-Polar Covalent Bonds:
Atoms share electrons equally.
Occurs when atoms are identical or have the same electronegativity (ability to attract electrons).
Polar Covalent Bonds:
Unequal sharing of electrons.
Causes a partial positive (\delta+) or negative (\delta-) charge for each atom or molecule (e.g., Water (H_2O): Oxygen is partially negative, Hydrogens are partially positive).
Ionic Bonds:
Form between ions.
Ion: An electrically charged atom or molecule.
Cation: A positively charged ion.
Anion: A negatively charged ion.
An ionic bond is an attraction between an anion and a cation.
Forms when one atom strips electrons from another (e.g., transfer of an electron from Sodium (Na) to Chlorine (Cl)).
After transfer, both atoms become charged ions.
Compounds formed by ionic bonds are called ionic compounds or salts (e.g., (NaCl) table salt, often found as crystals).
Hydrogen Bonds:
Form when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom.
In living cells, the electronegative partners are usually oxygen (O) or nitrogen (N) atoms (e.g., in Water (H2O) and Ammonia (NH3)).
Elements in Living Organisms
Nearly 100 different naturally occurring elements exist.
About 99\% of body weight consists of 6 elements:
Oxygen (O): 65\% of human weight. Part of water and most organic molecules; also molecular oxygen.
Carbon (C): 18\% of human weight. The backbone of all organic molecules.
Hydrogen (H): 10\% of human weight. Part of all organic molecules and of water.
Nitrogen (N): 3\% of human weight. Component of proteins and nucleic acids.
Calcium (Ca): 2\% of human weight. Constituent of bone; essential for nerve and muscle action.
Phosphorus (P): 1\% of human weight. Part of cell membranes, nucleic acids, and energy storage molecules; constituent of bone.
Water: The Molecule That Supports All Life
All living organisms require water more than any other substance.
The abundance of water makes Earth habitable.
Key Properties of Water (traced to hydrogen bonding):
Excellent Solvent:
Solution: A liquid that is a homogeneous mixture of substances.
Solvent: The dissolving agent of a solution.
Solute: The substance that is dissolved.
Aqueous Solution: One in which water is the solvent.
Water's versatility as a solvent is due to its polarity, allowing hydrogen bonds to form easily.
When an ionic compound dissolves, each ion is surrounded by a hydration shell of water molecules.
Water can also dissolve nonionic polar molecules and large polar molecules like proteins if they have ionic and polar regions.
Hydrophilic: Substance has an affinity for water.
Hydrophobic: Substance does not have an affinity for water.
Liquid at Body Temperature: Permits transport functions (e.g., blood is 90\% water). Main constituent of intracellular and extracellular spaces. About 60\% of body weight is water.
Can Absorb and Hold Heat Energy (High Specific Heat):
Heat is absorbed when hydrogen bonds break, and released when they form.
Minimizes temperature fluctuations, keeping them within limits that permit life.
Water absorbs and holds a lot of heat energy with only a modest increase in temperature, preventing rapid changes in body temperature.
Evaporation of Water Uses Up Heat Energy (Evaporative Cooling): Enables the body to lose excess heat quickly.
Participates in Essential Chemical Reactions:
Dehydration Synthesis (Condensation): Produces water molecules during the synthesis of biomolecules (carbohydrates, proteins, lipids).
Hydrolysis: Consumes water molecules during the breakdown of biomolecules (carbohydrates, proteins, lipids).
The Importance of Hydrogen Ions (pH)
A hydrogen atom in a hydrogen bond can shift from one water molecule to another.
The hydrogen atom leaves its electron behind and transfers as a proton or hydrogen ion (H^+). This forms a hydroxide ion (OH^-) and a hydronium ion (H3O^+). (2 H2O \rightleftharpoons H_3O^+ + OH^-).
Changes in concentrations of (H^+) and (OH^-) drastically affect cell chemistry.
In pure water, (H^+) and (OH^-) concentrations are equal.
Acids and Bases: Solutes that modify (H^+) and (OH^-) concentrations.
Acid: Any substance that increases the (H^+) concentration of a solution (donates hydrogen ions).
Base: Any substance that reduces the (H^+) concentration of a solution (accepts hydrogen ions or donates (OH^-)).
The pH Scale: Expresses hydrogen ion concentration.
Ranges from 0 to 14.
Acidic Solutions: pH values less than 7. Higher (H^+) concentration, lower pH.
Neutral Solutions: pH value of 7. (H^+) = (OH^-).
Basic Solutions (Alkaline): pH values greater than 7. Lower (H^+) concentration, higher pH.
Buffers: Minimize changes in (H^+) and (OH^-) concentrations to maintain stable pH in body fluids.
The internal pH of most living cells must remain close to pH \text{7}.
Example: Carbonic acid and bicarbonate are important buffer pairs in the body.
If blood is too acidic: (H2CO3 \to HCO_3^- + H^+) (Carbonic acid dissociates).
If blood is too alkaline: (HCO3^- + H^+ \to H2CO_3) (Bicarbonate accepts hydrogen ions).
The Organic Molecules of Living Organisms
Organic Molecules:
Made of carbon (C) and hydrogen (H).
May contain other elements like nitrogen (N), oxygen (O), phosphorus (P), or sulfur (S).
Held together by covalent bonds.
Carbon: The Backbone of Life:
Living organisms consist mostly of carbon-based compounds.
Carbon can form 4 covalent bonds with a variety of atoms, enabling it to form large, complex, and diverse molecules.
Can form single or double bonds.
In molecules with multiple carbons, each carbon bonded to 4 other atoms has a tetrahedral shape.
Molecular Diversity: Arises from carbon skeleton variations (length, branching, double bond position, presence of rings).
Macromolecule Synthesis and Breakdown:
Polymers: Large molecules made of repeating subunits called monomers.
Dehydration Synthesis (Condensation):
Occurs during the synthesis of biomolecules.
One subunit loses an -H and another subunit loses an -OH. A new covalent bond is formed, and water (H_2O) is lost.
Hydrolysis:
Occurs during the breakdown of biomolecules.
Water is consumed.
An -H is added to one subunit, and an -OH is added to another subunit.
Four Types of Organic Molecules (Macromolecules) in Organisms:
1. Carbohydrates
General Formula: (CH2O)n. Backbone of carbons with hydrogen and oxygen attached in the same proportion as water.
Functions:
Primary energy source for most organisms.
Structural support (e.g., cellulose in plant cell walls).
Monomers: Sugar monomers.
Types:
Monosaccharides (Simple Sugars):
Examples: Glucose (energy source for cells), Fructose, Galactose, Ribose (found in RNA), Deoxyribose (found in DNA).
Glucose monomers can be joined to form more complex carbohydrates.
Disaccharides: Two monosaccharides linked together via dehydration synthesis.
Examples: Sucrose (glucose + fructose), Maltose (glucose + glucose), Lactose (glucose + galactose).
Oligosaccharides: More than one monosaccharide linked together.
Polysaccharides: Thousands of monosaccharides joined in linear and/or branched chains.
Energy Storage:
Starch: Made in plants.
Glycogen: Made in animals.
Structural Support:
Cellulose: Indigestible polysaccharide made in plants for structural support.
2. Lipids
Characteristic: Do not dissolve in water (hydrophobic).
Distinguishing Feature: Not assembled by joining monomers to form polymers (unlike other macromolecules).
Three Important Classes of Lipids:
Triglycerides (Fats and Oils):
Structure: Composed of glycerol bonded to three fatty acids.
Fatty Acids:
Saturated (in fats): All single bonds between carbons. Tend to be solid at room temperature.
Unsaturated (in oils): Include some double bonds between carbons. Tend to be liquid at room temperature.
Function: Energy storage molecules. Stored in adipose tissue.
Phospholipids:
Structure: Glycerol plus two fatty acids and a phosphate group.
Possess a hydrophilic (water-loving) head and hydrophobic (water-fearing) tails.
Function: Primary component of cell membranes.
Steroids:
Structure: Carbon-based ring structures (comprising four fused rings).
Examples: Cholesterol, hormones (e.g., estrogen, testosterone).
3. Proteins
Structure: Long chains of subunits (monomers) called amino acids.
Amino Acids:
20 different types.
Each has an amino end, a carboxyl end, and an R group (side chain) that defines its unique properties.
Joined by peptide bonds, which are produced by dehydration synthesis reactions.
Peptide Bond: Forms between the carboxyl end of one amino acid and the amino end of the next amino acid.
Polypeptide: A polymer of 3-100 amino acids.
Protein: A polypeptide longer than 100 amino acids that has a complex structure and function.
Protein Function Depends on Structure (Levels of Protein Structure):
Primary Structure: The unique linear sequence of amino acids. Stabilized by peptide bonds.
Secondary Structure: Local folded patterns within the polypeptide chain.
Alpha helix or Beta pleated sheets.
Stabilized by hydrogen bonds between backbone atoms.
Tertiary Structure: The overall three-dimensional (3D) shape of a single polypeptide chain.
Stabilized by a combination of covalent bonds (e.g., disulfide bridges), ionic bonds, hydrophobic interactions, and hydrogen bonds.
Creates polar and nonpolar areas within the protein molecule.
Quaternary Structure: Occurs when two or more polypeptide chains (subunits) are joined to form a functional protein.
Denaturation:
Disruption of protein structure, leading to loss of function.
Can be caused by high temperature or changes in pH (e.g., heating an egg).
Enzymes:
Function as biological catalysts.
Speed up chemical reactions without being altered or consumed by the reaction.
Without enzymes, many biochemical reactions would not proceed quickly enough to sustain life.
4. Nucleic Acids
Structure: Long chains (polymers) containing monomer subunits known as nucleotides.
Functions: Store genetic information.
Types:
DNA (Deoxyribonucleic Acid): Contains the instructions for producing RNA.
RNA (Ribonucleic Acid): Contains the instructions for producing proteins.
Proteins, in turn, direct most life processes.
Flow of Genetic Information: DNA (nucleus) (\to) mRNA (cytoplasm) (\to) Protein (ribosome).
Nucleotides (Building Blocks of Nucleic Acids): Each nucleotide contains:
Five-carbon sugar:
Deoxyribose (in DNA nucleotides).
Ribose (in RNA nucleotides).
A nitrogenous base:
Pyrimidines (single-ring bases): Cytosine (C), Uracil (U) (only in RNA), Thymine (T) (only in DNA).
Purines (double-ring bases): Adenine (A), Guanine (G).
A phosphate group.
Deoxyribonucleic Acid (DNA):
Double-stranded nucleic acid.
Composed of deoxyribose sugar, phosphate group, and one of four nitrogenous bases ((A, T, C, G)).
Double strands are held together by hydrogen bonds that form between complementary bases:
Adenine (A) pairs with Thymine (T).
Guanine (G) pairs with Cytosine (C).
Runs antiparallel: the two backbones run opposite to one another.
Ribonucleic Acid (RNA):
Single-stranded nucleic acid.
Composed of ribose sugar, phosphate group, and one of four nitrogenous bases ((A, U, C, G)). (Uracil replaces Thymine).
Single strands (or regions within) can be held together by hydrogen bonds that form between complementary bases:
Adenine (A) pairs with Uracil (U).
Guanine (G) pairs with Cytosine (C).
Important Nucleotide: Adenosine Triphosphate (ATP)
ATP (Adenosine Triphosphate): The universal energy source for cells.
Energy Storage: The bonds between phosphate groups contain potential energy.
Energy Release: Breaking the terminal phosphate bond releases energy: (ATP \to ADP + P_i + Energy).
ATP Replenishment: ATP can be replenished from ADP (Adenosine Diphosphate) by using energy released during cellular chemical reactions to reattach a phosphate group: (ADP + P_i + Energy \to ATP).
DNA/Proteins as Tape Measures of Evolution
The linear sequences of nucleotides in DNA molecules are passed from parents to offspring.
Two closely related species are more similar in their DNA (and consequently their proteins) than are more distantly related species.
Molecular biology can be used to assess evolutionary kinship and relationships.