Fundamentals of Anatomy & Physiology - Chapter 2: The Chemical Level of Organization (Vocabulary Flashcards)
Overview
This note is a simpler summary of Chapter 2, "The Chemical Level of Organization," from Fundamentals of Anatomy & Physiology. It covers essential topics like what matter is, how atoms are built, different types of chemical bonds, how chemical reactions work, the role of enzymes, and the main types of organic and inorganic compounds vital for life. It also explains important ideas about water, pH, acids, bases, buffers, and the functions of carbohydrates, lipids, proteins, nucleic acids, and energy-carrying compounds in the body.
2-1 Atoms and Atomic Structure
Everything that takes up space and has weight is called matter. Matter is made of tiny particles called atoms, which then combine to form chemicals with specific characteristics. The way these chemicals behave at a tiny level affects how our body works (physiology).
Atoms are made up of even smaller subatomic particles:
Protons: Have a positive (+) charge and a mass of 1 unit.
Neutrons: Have no charge (neutral) and a mass of 1 unit.
Electrons: Have a negative (-) charge and a very tiny mass.
An atom's structure includes:
The nucleus: The central part, containing protons and neutrons.
The electron cloud: The space around the nucleus where electrons move. This is often shown as electron shells or energy levels, which are like layers where electrons are likely to be found.
An element is a pure substance made only of one type of atom. The atomic number, which is the number of protons, mostly decides an element's chemical properties. Isotopes are different versions of the same element that have the same number of protons but different numbers of neutrons, meaning they have different mass numbers (protons + neutrons).
Electrons occupy different energy levels or shells: the first shell can hold up to 2 electrons, and the second and third shells can each hold up to 8 electrons. The very outermost shell is called the valence shell, and the electrons in this shell largely determine how an atom will bond with other atoms. For example, sodium has 11 protons, so thinking about its electron arrangement helps predict how it will react.
Our bodies contain several key elements:
Major elements (by weight):
Oxygen (65%): Part of water and many other molecules; its gas form is vital for breathing.
Carbon (18.6%): Found in all organic (living) molecules.
Hydrogen (9.7%): Part of water and most body compounds.
Nitrogen (3.2%): Found in proteins, DNA, and other organic molecules.
Calcium (1.8%): Important for bones, teeth, cell membranes, nerve signals, muscle contractions, and blood clotting.
Phosphorus (1.0%): Found in bones, teeth, DNA, and high-energy compounds like ATP.
Potassium (0.4%): Essential for cell membrane function, nerve signals, and muscle contraction.
Trace elements (present in small amounts):
Sodium (0.2%) and Chlorine (0.2%): Help regulate blood volume.
Magnesium (0.06%), Sulfur (0.04%), Iron (0.007%), Iodine (0.0002%): Have various roles, including assisting enzymes and oxygen transport.
Many others like silicon, fluorine, copper, manganese, zinc, selenium, cobalt, molybdenum, cadmium, chromium, tin, aluminum, boron, and vanadium. The roles of many of these are still being studied.
For example, hydrogen has isotopes: Hydrogen-1 (protium) has 0 neutrons, Hydrogen-2 (deuterium) has 1 neutron, and Hydrogen-3 (tritium) has 2 neutrons. All have 1 proton.
The number of electrons in the outermost shell dictates how an atom will react. Shells fill up from the inside out, and the valence shell is key for forming bonds.
2-2 Molecules and Compounds
A molecule is formed when two or more atoms are held together by strong chemical bonds. A compound is a molecule made up of two or more atoms from different elements also joined by bonds. So, while all compounds are molecules, not all molecules are compounds (e.g., O2 is a molecule but not a compound, H2O is both a molecule and a compound).
The molecular weight of a molecule or compound is found by adding up the atomic weights of all its atoms.
Chemical bonds are formed when atoms share, gain, or lose electrons. There are three main types:
Ionic bonds: These form between ions. An electron donor gives away electrons and becomes a positively charged ion (cation). An electron acceptor gains those electrons and becomes a negatively charged ion (anion). Ionic bonds are the attraction between these oppositely charged ions. A good example is table salt (sodium chloride, NaCl): Sodium (Na) gives an electron to chlorine (Cl), forming Na$^+$ and Cl$^-$, which then attract each other to make NaCl.
Covalent bonds: These are strong bonds where atoms share electrons. A single covalent bond shares one pair of electrons, a double covalent bond shares two pairs, and a triple covalent bond shares three pairs. Covalent bonds can be:
Nonpolar: Electrons are shared equally between atoms.
Polar: Electrons are shared unequally, creating slight positive and negative charges on different parts of the molecule. Water is a great example of a polar molecule. Oxygen pulls electrons more strongly than hydrogen, giving oxygen a slight negative charge and hydrogens slight positive charges.
Hydrogen bonds: These are weak attractions between nearby polar molecules. They happen because of the attraction between a slight positive charge on one molecule and a slight negative charge on another. Hydrogen bonds are what make water molecules stick together (cohesion) and create surface tension. They're also important for the shapes of many biological molecules. In water, covalent bonds hold the H and O atoms together within one water molecule, while hydrogen bonds link separate water molecules.
2-3 Chemical Reactions
In our bodies, most reactions don't just happen on their own; they need a push. This push is called activation energy. Enzymes, which are special proteins, help by lowering this activation energy, making reactions happen much faster without getting used up themselves.
Reactants are the starting materials of a reaction.
Products are the materials 만들어d by the reaction.
Metabolism refers to all the chemical reactions happening in the body at any given time.
There are several types of chemical reactions:
Decomposition (Catabolism): Breaks larger molecules into smaller ones. AB \rightarrow A + B (e.g., digestion).
Hydrolysis: A decomposition reaction that uses water. AB + H_2O \rightarrow AH + BOH.
Synthesis (Anabolism): Builds larger molecules from smaller ones. A + B \rightarrow AB (e.g., building muscle).
Dehydration synthesis (Condensation): A synthesis reaction that removes water. AH + BOH \rightarrow AB + H_2O.
Exchange reactions: Involve breaking bonds and then forming new ones. AB + CD \rightarrow AD + CB. (It's like partners swapping in a dance).
Reversible reactions can go in both directions: A + B \rightleftharpoons AB. Eventually, these reactions reach equilibrium, where the amounts of reactants and products become stable, even though the forward and reverse reactions are still happening. If you add or remove substances, the system will adjust to find a new balance. A good example is how your body handles carbon dioxide in the blood: CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons HCO_3^- + H^+.
2-4 Enzymes
Chemical reactions in our cells need help to get started (they need to overcome activation energy). Enzymes are specialized proteins that act as catalysts. They lower the activation energy, making reactions happen much faster without being used up themselves. Think of them as tiny tools that speed things up.
Substrates are the specific molecules that an enzyme acts upon. They fit into a special pocket on the enzyme called the active site.
When a substrate binds to an active site, it forms an enzyme–substrate complex, which quickly turns the substrate into a product.
After the product is released, the enzyme is ready to help another substrate.
Enzymes have key features:
Specificity: Each enzyme usually only speeds up one particular type of reaction.
Saturation limits: There's a maximum rate at which an enzyme can work because there are only so many active sites. If there are too many substrates, the enzyme might get "saturated."
Regulation: Cells can control enzyme activity to manage their metabolism.
2-5 Inorganic and Organic Compounds
Nutrients are essential molecules our body gets from food.
Metabolites are molecules that are either made or broken down within the body.
Compounds are broadly divided into two groups:
Inorganic compounds: These generally do not contain both carbon and hydrogen (though some, like CO_2, have carbon). Examples include carbon dioxide, oxygen, water, and inorganic acids, bases, and salts.
Organic compounds: These are built around chains of carbon and hydrogen atoms. They are typically larger and more complex. Major examples essential for life include carbohydrates, lipids, proteins (made of amino acids), and nucleic acids (DNA and RNA).
2-6 Properties of Water
Water makes up roughly two-thirds of our body weight and is incredibly important for many reasons:
Solvent properties: Water is an excellent solvent, meaning it can dissolve many substances to form solutions (uniform mixtures where solutes are dissolved in a solvent).
Polarity: Water molecules are polar (they have slight positive and negative ends). This polarity allows water to surrounded other charged molecules or ions, forming hydration spheres around them and keeping them dissolved.
Ionization: Many inorganic compounds break apart into ions (electrically charged atoms) when dissolved in water.
Hydrophilic vs. Hydrophobic: Molecules that dissolve well in water are hydrophilic ("water-loving"). Molecules that do not dissolve in water (like oils) are hydrophobic ("water-fearing").
Electrolytes: These are inorganic ions in solution that can conduct electricity. Imbalances in electrolytes can be very harmful.
Chemical reactivity: Water is often a reactant or product in important chemical reactions within the body (e.g., hydrolysis).
High heat capacity: Water can absorb and release a lot of heat with only a small change in its own temperature. This helps keep our body temperature stable.
Lubrication: Water moistens surfaces and reduces friction, acting as a lubricant (e.g., in joints).
In water, large numbers of phospholipids and glycolipids (components of cell membranes) can form micelles, which are little spheres where the water-loving (hydrophilic) heads face outwards toward the water, and the water-fearing (hydrophobic) tails hide inside.
2-7 pH and Homeostasis
pH is a measure of how acidic or basic a solution is. It's related to the concentration of hydrogen ions (H⁺):
More H⁺ ions means a lower pH and a more acidic solution.
Fewer H⁺ ions means a higher pH and a more basic (or alkaline) solution.
A neutral pH means there's an equal balance of H⁺ and hydroxide ions (OH⁻). Pure water has a neutral pH of 7.0.
For human blood, the normal pH range is very narrow, from about 7.35 to 7.45. Maintaining this specific pH is crucial for homeostasis (keeping the body's internal environment stable), because many bodily processes are sensitive to pH changes.
2-8 Acids, Bases, and Salts
An acid is a substance that releases hydrogen ions (H⁺) into a solution. Strong acids break apart completely in water. Example: Hydrochloric acid (HCl) in the stomach.
A base is a substance that accepts hydrogen ions (H⁺) from a solution. Strong bases also break apart completely. Example: Sodium hydroxide (NaOH).
Weak acids and weak bases do not dissociate (break apart) completely in water. They play a crucial role in helping to keep pH balanced.
A salt is a substance that breaks apart in water to form ions other than H⁺ or OH⁻ (e.g., NaCl dissociates into Na$^+$ and Cl$^- $).
Buffers are mixtures of weak acids and bases that help resist changes in pH. When the acid level rises, the base component of the buffer absorbs the extra H⁺; when the acid level drops, the acid component releases H⁺. The carbonic acid–bicarbonate buffer system is very important for maintaining blood pH. Antacids, like those containing sodium bicarbonate, work by neutralizing stomach acid.
2-10 Carbohydrates
Carbohydrates are organic molecules made of hydrogen, carbon, and oxygen, usually in a ratio of 1 carbon to 2 hydrogen to 1 oxygen (C:H:O = 1:2:1). Some carbohydrates are isomers, meaning they have the same chemical formula but different structures. Carbohydrates are primarily used for quick energy and also help build cell structures.
They come in different sizes:
Monosaccharides: Simple sugars with three to seven carbon atoms. Examples: glucose (main energy source for cells), fructose, and galactose.
Disaccharides: Formed by joining two monosaccharides together, typically by dehydration synthesis (removing water). Examples: sucrose (table sugar) and maltose.
Polysaccharides: Large complex carbohydrates made of many sugar units linked together by dehydration synthesis. Examples: glycogen (how animals store glucose), starch (how plants store glucose), and cellulose (plant cell walls).
2-11 Lipids
Lipids are organic molecules, mostly made of carbon and hydrogen, that are generally hydrophobic (don't mix with water). They include fatty acids, eicosanoids, glycerides, steroids, phospholipids, and glycolipids.
Fatty acids: Long chains of carbon and hydrogen with a carboxyl group (–COOH) at one end. They are mostly nonpolar. They can be:
Saturated: Have only single bonds between carbon atoms in their tail, making the chain straight.
Unsaturated: Have one or more double bonds in their tail, which causes bends in the chain. If one double bond, it's monounsaturated; if more than one, it's polyunsaturated.
Eicosanoids: Important signaling molecules (like hormones) derived from a fatty acid called arachidonic acid. They are vital for things like immune responses and inflammation. Some must come from our diet.
Glycerides: Fatty acids attached to a glycerol molecule.
Monoglyceride: One fatty acid attached to glycerol.
Diglyceride: Two fatty acids attached to glycerol.
Triglyceride: Three fatty acids attached to glycerol. Also called triacylglycerols or neutral fats. They are major energy storage, provide insulation, and protect organs. They are formed by dehydration synthesis and broken down by hydrolysis.
Steroids: Unique lipids with a distinctive four-ring carbon structure. They serve various roles, including being part of cell membranes (like cholesterol), acting as hormones (sex hormones like estrogen and testosterone), corticosteroids, calcitriol, and bile salts (for fat digestion).
Phospholipids and Glycolipids: These are crucial components of cell membranes.
Phospholipids: Have a diglyceride base, a phosphate group, and a nonlipid group attached. They have a water-loving (hydrophilic) head and two water-fearing (hydrophobic) tails.
Glycolipids: Have a carbohydrate group attached instead of a phosphate group. They also have hydrophilic heads and hydrophobic tails.
In water, both can form micelles, small spheres with heads facing out and tails facing in.
2-12 Proteins
Proteins are the most abundant and diverse organic molecules in the body, made primarily of carbon, hydrogen, oxygen, and nitrogen. They are built from 20 different types of amino acids, which are like the building blocks. When amino acids link up, they form a chain called a polypeptide, which then folds into a protein.
Proteins have many vital functions:
Structural support: Form skin, hair, muscles, etc.
Movement: Contractile proteins in muscles allow movement.
Transport: Carrier proteins move substances in and out of cells (e.g., hemoglobin transports oxygen).
Buffering: Help regulate the body's pH.
Metabolic regulation: Enzymes, which are proteins, speed up chemical reactions.
Coordination and control: Hormones (many of which are proteins) carry messages throughout the body.
Defense: Antibodies help fight off infections.
All amino acids share a basic structure: a central carbon atom, a hydrogen atom, an amino group (–NH₂), a carboxyl group (–COOH), and a unique side chain (R group) that makes each amino acid different. Amino acids are linked together by dehydration synthesis, forming peptide bonds to create dipeptides (two amino acids), tripeptides (three), and longer polypeptides.
Protein structure is complex and described in four levels:
Primary structure: The simple, linear sequence of amino acids in the polypeptide chain.
Secondary structure: Local folding patterns that result from hydrogen bonds between amino acids. Common patterns are the alpha helix (a spiral) and the beta sheet (a folded, pleated structure).
Tertiary structure: The overall three-dimensional shape of a single polypeptide chain, formed by interactions between the R groups (side chains).
Quaternary structure: Occurs when multiple polypeptide chains (subunits) come together and interact to form a functional protein (e.g., hemoglobin).
Proteins can be globular (water-soluble, often enzymes or transport proteins) or fibrous (long, insoluble, structural proteins like collagen).
As mentioned, enzymes are protein catalysts that lower activation energy, speeding up reactions without being used up. Substrates bind to the enzyme's active site to form an enzyme–substrate complex, which helps create products faster. Enzymes are specific to certain reactions, can become saturated if there are too many substrates, and their activity is regulated by the cell. Their function depends heavily on things like substrate and enzyme concentration, temperature (high heat can cause denaturation, where the protein loses its shape and function), and pH (each enzyme works best at a specific pH).
Glycoproteins are proteins with attached carbohydrate groups, found in enzymes, antibodies, hormones, and cell membranes. Proteoglycans are large sugar molecules attached to polypeptides, which contribute to the thick, jelly-like consistency of body fluids.
2-13 Nucleic Acids
Nucleic acids are molecules that store and process our genetic information.
DNA (Deoxyribonucleic Acid): Stores genetic instructions for the long term, directing how proteins are made and controlling cell metabolism.
RNA (Ribonucleic Acid): Involved in the immediate steps of making proteins.
Both DNA and RNA are built from smaller units called nucleotides. Each nucleotide has three parts:
A pentose sugar: Deoxyribose in DNA, ribose in RNA.
A phosphate group.
A nitrogenous base: Adenine (A), Guanine (G), Cytosine (C), and Thymine (T) in DNA; Adenine (A), Guanine (G), Cytosine (C), and Uracil (U) in RNA (U replaces T in RNA).
DNA typically consists of two long chains of nucleotides that are twisted around each other to form a double helix. These two chains are held together by hydrogen bonds between specific pairs of bases: Adenine (A) always pairs with Thymine (T), and Cytosine (C) always pairs with Guanine (G).
RNA usually consists of a single chain of nucleotides. There are three main types:
Messenger RNA (mRNA): Carries genetic instructions from DNA to the protein-making machinery.
Transfer RNA (tRNA): Helps bring amino acids to the ribosome during protein synthesis.
Ribosomal RNA (rRNA): A component of ribosomes, where proteins are made.
In RNA, the base pairing rule is A with U (Uracil) and C with G. The specific sequence of these bases in DNA and RNA contains all our genetic information, which is vital for inheritance, replication, and protein synthesis.
2-14 High-Energy Compounds
Many molecules that carry energy in the cell are derived from nucleotides. Phosphorylation is the process of adding a phosphate group to a molecule, which creates high-energy bonds capable of storing a lot of energy.
The most important energy carrier in the cell is ATP (adenosine triphosphate).
AMP (adenosine monophosphate) has one phosphate group.
ADP (adenosine diphosphate) has two phosphate groups.
ATP has three phosphate groups. The bonds between these phosphate groups are "high-energy" bonds.
When ATP is broken down (hydrolyzed) into ADP and an inorganic phosphate group by an enzyme called ATPase, it releases usable energy that cells can use to power almost all their activities (e.g., muscle contraction, active transport). The reaction can be thought of as: \text{AMP} \rightarrow \text{ADP} \rightarrow \text{ATP} + \text{P}_i (This sequence shows how phosphate groups can be added step-by-step; ATP hydrolysis releases energy). AT Pases are crucial for releasing this stored energy.