Chemistry of Life

Introduction to Matter Humans are made of elements; the simplest form of matter. Cannot be broken down to other substances by chemical reactions.

Elements of Life Most of the mass of the human body is made up of only a few elements, called the “elements of life” Element % of Body Weight Significance Oxygen, O 65 Part of water; Needed for cellular respiration. Carbon, C 18.5 Backbone of all organic molecules. Hydrogen, H 9.5 Found in nearly every compound in the body. Nitrogen, N 3.2 Part of proteins and nucleic acids. Calcium, Ca 1.5 Bones, teeth, used in nerve impulses and to signal muscle contraction. Phosphorus, P 1.0 Bones, teeth, nucleic acids, and ATP (energy molecule).

The lack of an element in the diet can cause a mineral deficiency. The human body also contains many trace elements at levels of less than 1.0%. The lack of an element in the diet can cause a mineral deficiency. Bone density loss due to calcium deficiency Enlarged thyroid caused by iodine deficiency Anemia caused by iron deficiency

Atoms are made of three particles, two in the nucleus: Elements are made of atoms, the smallest particles of an element that still have all of its properties. Atoms are extremely small; 100 million atoms laid side-by-side would only make a row one centimeter long. Atoms are made of three particles, two in the nucleus: Protons are positively charged particles (+) that determine the atom’s identity. Neutrons are particles that carry no charge and determine the atom’s mass.

Electrons determine how reactive an atom will be with other atoms. Electrons are negatively charged particles (–) with only 1/1840 the mass of a proton. Electrons are in constant motion in the space surrounding the nucleus. Electrons determine how reactive an atom will be with other atoms. Label diagram to right with protons, neutrons, electrons and nucleus.

Models of atoms The most commonly used way to draw atoms is the planetary, or electron- shell model. This method makes it easier to see the electrons and how they interact with other atoms during chemical reactions. The electron-shell model is inaccurate because electrons are constantly in motion and the atom is mostly empty space.

Atoms in larger molecules may also be drawn using a space-filling model. An electron cloud is drawn around the nucleus, which cannot be seen. This is useful for showing molecular shape and interactions between molecules.

Classification of Matter Neutral atoms have equal numbers of protons and electrons. The positive and negative charges cancel each other out, leaving no net charge across the atom.

Ions Ions are atoms that have gained or lost an electron, giving them a charge. Ions that have lost an electron are positively-charged. Ions that have gained an electron are negatively-charged.

Ions found in cells or fluids in the body are called electrolytes. Na+ (sodium), found in tears, sweat, blood. K+ (potassium), found in nerve cells, blood. Ca++ (calcium), found in blood, nerve cells, muscle cells, bone. Cl- (chloride), found in blood and stomach acid. Electrolytes are included in sports drinks to replace what is lost through sweat.

Compounds and Mixtures Most substances in the human body are not pure elements -- they are part of a compound, a substance consisting of two or more elements. For example, the lungs exchange oxygen (an element) for carbon dioxide (a compound).

Compounds and elements may also be present in the same place but not chemically combined. This is called a mixture. Plasma is a mixture of 92% water, 7% proteins, and 1% sugars, electrolytes, and fats.

Chemical Bonds Atoms are stable when their outermost shell of electrons, called valence electrons, is full. Atoms achieve this stability through interactions of their electrons called chemical bonds.

Sodium chloride (NaCl) Ionic bonds are formed when atoms gain or lose electrons. The resulting ions have opposite charges and attract each other. Sodium atom (an uncharged atom) Chlorine atom (an uncharged atom) Sodium chloride (NaCl) Na+ Cl– Sodium ion Chlorine ion

Atoms can form covalent bonds by sharing electrons with another element. Most compounds in the human body are formed with covalent bonds. Hydrogen atoms (2 H) Hydrogen molecule (H2)

Covalent bonds can be drawn in three ways: An electron-shell model, where the location of any shared valence electrons are drawn. A structural formula, where bonds are shown with lines – A space-filling model, where the two electron clouds are merged together.

The most common method in textbooks is the structural formula. Single covalent bonds share one pair of electrons and are drawn with one line. A double covalent bonds share two pairs of electrons and are drawn with two lines. A triple covalent bond, is the sharing of three pairs of valence electrons. This has three lines.

A hydrogen bond occurs when two polar compounds that contain charged areas attract each other. Polar molecules have a positive and negative side.

Properties of Water Water is a polar molecule, meaning it has both positive and negative ends (poles). This enables water to form hydrogen bonds with itself, resulting in many unique properties.

Cohesion is the attraction between molecules of water.

Adhesion is the attraction of water to the molecules of the container or tube it is in.

Water has a very high heat capacity, meaning a large amount of heat energy is required to raise its temperature. This is important during perspiration, as sweat will gather and release a lot of heat energy as it evaporates.

Water also known as the universal solvent because it can dissolve any ionic compound or polar covalent compound.

Any substance that dissolves in water is called a solute. The resulting mixture of solvent and solute is called a solution. Ringer’s solution: Sodium ion, chloride ion, lactate, potassium ion, calcium ion, water.

Acids and Bases Molecules like water can dissociate, meaning they break apart into hydrogen ions (H+) and hydroxide ions (OH-). Acids release greater concentrations of H+ ions. Bases release greater concentrations of OH- ions. Neutral solutions, like water, have equal amounts of each.

The pH scale measures the concentration of H+ ions in a solution. A low pH (acidic) means a higher concentration of H+ ions. A high pH (basic) means a lower concentration of H+ ions.

pH and Homeostasis Each body fluid has a specific pH range that is constantly maintained by the body. Blood: 7.35-7.45 Sweat: 4.0-6.8 Saliva: About 6.0 Semen: 7.2-8.0

Blood and other body fluids contain buffer systems, which can restore pH homeostasis. The bicarbonate buffering system stores pH by either altering respiration rate in the lungs or excretion through the kidneys.

Organic Chemistry Organic compounds, those found in living organisms, are primarily composed of covalent bonds, as they are the strongest and most stable. The element carbon, with exactly 4 valence electrons, is the backbone all organic compounds. Able to share all four electrons and form up to four separate bonds.

Most organic molecules are polymers, or a molecules made up of repeating parts. Each repeating unit within a polymer is called a monomer.

Nucleic Acids A nucleic acid is made of repeating units called nucleotides. Each nucleotide is made of: A phosphate (PO4) group. A nitrogen-containing base. A 5-carbon sugar.

There are five types of nucleotides found in nucleic acids. The primary difference between them is the nitrogenous base. The sequence of a nucleic acid is described using the first letter of each nucleotide. AGC = Adenine – Guanine - Cytosine

DNA is a double-helix nucleic acid that contains the genetic information for all living organisms. The sugar and phosphate groups form the helix- shaped strands or “backbones” of the molecule. The nitrogenous bases connect each strand and form the code used in protein synthesis.

RNA is similar to DNA, with three important differences: It is a single-stranded molecule The base thymine (T) is not used; uracil (U) is used instead. Ribose is used in place of deoxyribose as the sugar.

ATP ATP is nucleotide that is not found in DNA or RNA, but it is used by cells to transfer energy. The bond that connects the third phosphate to ADP is very high energy, and can be broken when the cell needs to perform work.

Carbohydrates Carbohydrates are organic molecules that contain carbon, hydrogen, and oxygen in a 1:2:1 ratio. Carbohydrates may serve as an energy source or as part of the structure of living organisms.

Monosaccharides, the simplest carbohydrate, made from only one sugar molecule. Glucose, also called blood sugar, is one example. Monosaccharides are used as a short- term energy source in many organisms.

Each disaccharide is an energy storage molecule. Disaccharides are molecules made of two monosaccharides bonded together. Sucrose is table sugar. Lactose is the sugar found in milk. Maltose is found in germinating seeds and is used to brew beer. Each disaccharide is an energy storage molecule.

Polysaccharides are complex sugars, made of three or more monosaccharides joined together.

Starch is a storage polysaccharide of plants.

Glycogen is a storage polysaccharide found in the muscle and liver of humans. Structurally similar to starch, except that the molecule branches off more.

Cellulose is a structural carbohydrate found in plant cell walls. Allows plants to be sturdy and rigid.

Cellulose has a different chemical structure than starch and glycogen, and is only digestible by certain types of animals. Cows have a massive stomach that holds ingested plant material and bacteria that digests it for them.

Chitin is a structural polysaccharide similar in structure to cellulose. Found in the exoskeleton of insects and the cell walls of fungi.

Lipids Lipids are organic molecules made mostly of carbon and hydrogen. Most lipids are hydrophobic, meaning they do not dissolve in water.

Most lipids are made up of long chains of carbon atoms called fatty acids. Saturated fatty acids have the maximum number of hydrogen atoms possible, no double bonds, and are solids at room temperature.

Unsaturated fatty acids have one or more double bonds. Unsaturated fats usually come from plant sources or fish and are liquid at room temperature.

Triglycerides Triglycerides are the biggest component of plant and animal fat. They are made of glycerol, a 3-carbon alcohol, and three fatty acids.

Triglycerides are the most common type of lipid in the body. Found under the skin as an energy reserve and insulation. Surround organs like the heart to provide cushioning and protection.

Phospholipids Phospholipids are similar to triglycerides, but one of the fatty acids is replaced by a charged phosphate (PO4) group.

The phosphate “head” is hydrophilic, meaning it is polar and will dissolve in water. The two fatty acid “tails” are hydrophobic, meaning they are nonpolar and do not dissolve in water.

Phospholipids tend to arrange themselves in water bilayers, liposomes, or micelles to minimize the exposure of the hydrophobic tails to the water.

Steroids Steroids have a structure completely different than other lipids – they have four interlocking carbon rings. Many hormones are steroids, such as testosterone, cortisol, and estrogen.

Proteins Category Function Example Support Provide framework for the body. Collagen in ligaments. Movement Contract and create movement. Skeletal muscle. Transport Transport of materials in and out of cells. Glucose transporter in cell membranes. Buffering Prevent changes in pH. Proteins in blood plasma. Metabolic regulation Speed up the rate of chemical reactions. Digestive enzymes, in the stomach. Coordination Signal changes throughout the body. Hormones, such as insulin. Defense Protect against viruses and bacteria. Antibodies in blood. Proteins are polymers made of amino acids, and have a wide variety of functions.

Amino acids all have a central carbon atom surrounded by four groups. The R-group is a variable group, and the only difference between the 20 different amino acids found in humans.

Those 20 amino acids can be combined in nearly an infinite number of different combinations. The sequence of amino acids determines the shape of the protein, which then determines the protein’s function. Hemoglobin is a globular protein found in red blood cells. Keratin is a long, fibrous protein found in the skin and nails.

Since morphine has a similar shape to endorphin, it can be administered as a pain reliever.

Any change that permanently alters a protein’s shape is called denaturation. As the shape of the protein changes, it loses its original function.

Enzymes Enzymes are special proteins that catalyze, or speed up the rate of chemical reactions in the body. Substrates bind to the enzymes and are converted into products.

Enzymes lower activation energy; the minimum amount of energy needed to initiate a chemical reaction. Lower activation energy means the reaction occurs more easily, quickly, and more often.

Enzymes, like other proteins, must maintain a certain shape to function. The lock-and-key theory states that a substrate must exactly match an active size of an enzyme to activate it. If an enzyme denatures and changes its shape, it will no longer function with the substrate.