Chapter 2: Atoms, Ions, and Molecules

Phospholipids

- amphipathic molecules that form chemical barriers of cell membranes - composed of glycerol, two fatty acids, a phosphate, and various organic groups - glycerol, phosphate, and organic groups form a hydrophilic polar head, and fatty acids form two hydrophobic non polar tails

What are the functions of proteins?

- catalysts (enzymes) - defense -transport - support - movement - regulation - storage

Adenosine triphosphate (ATP)

- composed of the nitrogenous base adenine, a ribose sugar, and three phosphate groups - fcn: central molecule in the transfer of chemical energy within cells

Hydrogen bond

- forms between polar molecules (intermolecular) - between a partially positive hydrogen atom and a partially negative atom (usually o2) - individually weak, but collectively strong

Steroids

- includes cholesterol, steroid hormones, and bile salts - four rings composed mainly of hydrocarbons that differ in the side chains extending from the rings - fcn: cholesterol is the precursor for synthesis of other steroids, steroid hormones are released by endocrine glands, and bile salts facilitate micelle formation in the digestive tract

Eicosanoids

- locally acting signaling molecules associated with all body systems - primarily functions in the inflammatory response of the immune system and communications with the nervous system - modified 20-carbon fatty acids synthesized from arachidonic acid

Triglycerides

- the most common form of lipid in living things - fcn: long-term energy storage in adipose CT and structural support, cushioning, and insulation of the body - formed from a glycerol molecule and three fatty acids that vary in length and number of double bonds between carbons; formed by the process of dehydration synthesis

Non polar, polar, and amphipathic molecules

-non polar: contain non polar covalent bonds, which are formed between the same elements ex: oxygen, carbon dioxide, and triglycerides -polar: polar covalent bonds, which contain different elements that are bound together ex: water, glucose -amphipathic: contains both non polar and polar components ex: phospholipids

What are the 2 classes of nucleic acids?

1. DNA (double stranded, contains thymine, found in chromosomes within the nucleus and within the mitochondria) 2. RNA (single stranded, contains uracil, located within the cytoplasm) - both are polymers composed of nucleotide monomers - nucleotide monomers are linked by a phosphodiester bond

What are the four organic biological macromolecules (biomolecules)?

1. Lipids 2. Carbohydrates 3. Nuclei acids 4. Proteins

What are the major elements? (collectively they compose more than 98% of body weight)

1. Oxygen 2. Carbon 3. Hydrogen 4. Nitrogen 5. Calcium 6. Phosphorus

What are the 3 subatomic particles?

1. Protons (+) 2. Neutrons 3. Electrons (-)

General rules for assigning charges

1. atoms with one, two, or three electrons in the outer shell generally donate electrons and become cations 2. atoms with five, six, or seven electrons in the outer shell tend to accept electrons and become anions

Carbohydrates (from least to most complex)

1. monosaccarides: simple sugar monomers (e.g., glucose, galactose, fructose, ribose, and deoxyribose) 2. disaccharides: formed from two monosaccharides (e.g., sucrose, lactose, and maltose) 3. polysaccharides: many monosaccarides (e.g., glycogen)

Describe the 4 types of protein structure

1. primary: linear sequence of amino acids joined by peptide bonds 2. secondary: structural patterns within a protein that result from hydrogen bonds formed between amino acids, which may include alpha helixes (spiral coil) and beta-pleated sheets 3. tertiary: the completed 3-D shape or conformation of the protein, which may be a fibrous or globular protein 4. quaternary: two or more protein molecules associate to form the final protein

What are the 3 components of a nucleotide monomer?

1. sugar 2. phosphate 3. nitrogenous base

4 functions of water as a liquid

1. transports 2. lubricates 3. cushions 4. excretes wastes

What are the 4 primary classes of lipids?

1. triglycerides 2. phospholipids 3. steroids 4. eicosanoids * other lipids include glycolipids and fat-soluble vitamins (A, E, K)

Matter

A substance that has mass and occupies space. Three forms: 1. Solid (bone) 2. Liquid (blood) 3. Gas (oxygen, carbon dioxide)

Atom

All matter is composed of atoms, which are the smallest particles that exhibit the chemical properties of an element.

Cation

Ion with a + charge that results from losing or donating an electron ex: sodium, potassium, calcium, magnesium, hydrogen

Anion

Ion with a - charge that results from gaining or accepting an electron ex: chloride, bicarbonate, phosphate

Water can spontaneously dissociate to form ______?

Ions ex: H2O--> (H+) + (OH-)

Lipogenesis and lipolysis

Lipogenesis occurs through a dehydration synthesis reaction that involves the removal of a water molecule between each fatty acid and a glycerol. Lipolysis is a hydrolysis reaction that splits the glycerol and three fatty acids by the addition of water at each of the fatty acids.

Physical half life vs. biological half life

Physical: the time it takes for 50% of the radioisotope to become stable (few hours to thousands of years) Biological: the time required for half of the radioactive material to be eliminated from the body

Covalent bond

The bond that is formed when atoms share electrons in order to become stable. The four most common elements that form covalent bonds are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). The bond formed can be a single, double, or triple covalent bond.

Solution

a homogenous mixture in which the substance is smaller than 1 nanometer, and it dissolves in water ex: blood plasma

Glycogen

a polysaccharide composed of multiple glucose monomers by a process called glycogenesis - stored in the liver and breaks down as needed to release glucose into the blood

Glucose

a six-carbon (hexose) that is the most common monosaccharide fcn: primary nutrient supplying energy to cells - excess glucose is absorbed by the liver and skeletal muscle tissue

Emulsion

a suspension specifically composed of water (or other polar substance) and a non polar liquid, such as vegetable oil, that only mix when agitated ex: breast milk

Base

accepts H+ when added to a solution; proton acceptor; decreases the amount of H+ free in solution; pH > 7

Hydrolysis

addition of a water molecule during the digestion of complex molecules to form simpler components

Inorganic molecules

all other types of molecules that aren't organic including water, salts, acids, and bases

Specific heat

amount of energy required to increase the temperature of 1 gram of a substance by 1 degree Celsius (C)

What substances partially dissolve in water?

amphipathic molecules that have both polar and non polar regions (e.g., phospholipids)

The octet rule

atoms obtain an outer shell with eight electrons and gain chemical stability through the loss, gain, or sharing of electrons

Ions

atoms or groups of atoms with a +/- charge and are produced from the loss or gain of electrons

Cohesion

attraction between water molecules

Adhesion

attraction between water molecules and a substance other than water

Ionic bond

binding of cation+anion by an electrostatic interaction to form salts ex: (Na+)+(Cl-)= NaCl (an ionic compound)

What do biomolecules always contain?

carbon, hydrogen, and oxygen may have 1 or more of the following: nitrogen, phosphorus, or sulfur

Mixtures

combining of two or more substances that are (1) not chemically changed (2) and can be separated by physical means (evaporation or filtering) includes: suspensions, colloids, and solutions

Structural formula

complementary to the molecule's molecular formula and exhibits not only the numbers and types of atoms but also their arrangements within the molecule; provide a means for differentiating isomers ex: the molecular formula for carbon dioxide is CO2 and its complementary structural formula O=C=O

Colloid

composed of a protein within water that ranges in size from 1 to 100 nanometers; remains mixed when not in motion ex: cell cytosol and proteins within blood plasma

Polyatomic ions

composed of more than one atom ex: bicarbonate, phosphate

Denaturation

conformational change to a protein - normally irreversible - occurs during heating or with a pH change (+/-)

Radioisotope

contain and excess number of neurons, making them unstable ex: alpha and beta particles, gamma rays

Isotope

different atoms of the same element that have the same number of protons and electrons but differ in the number of neutrons (therefore they have different atomic masses) ex: carbon

Atomic number

exhibits the number of protons in an atom and is located above an elements symbol

3 phases of water

gas (water vapor), liquid (water), and solid (ice)

Heat of vaporization

heat required for the release of molecules from a liquid phase into the gaseous phase for 1 gram of a substance

Electronegativity

how atoms share electrons in a covalent bond -nonpolar: equal sharing of electrons -polar: unequal sharing of electrons Electronegativity increases both from left to right across a row of the periodic table and from the bottom to top in a column.

Arrange the four most common elements from least to greatest according to their electronegativity

hydrogen < carbon < nitrogen < oxygen

Surface tension

inward pulling of cohesive forces at the surface of water

Glycolipids

lipid molecules with carbohydrate attached fcn: cell binding to form tissues

Isomers

molecules composed of the same number and kind of elements but arranged differently in space ex: glucose, galactose, and fructose all have the same chemical formula (6 carbon atoms, 12 hydrogen atoms, and 6 oxygen atoms) but different structural formulas

Molecular compound

molecules composed of two or more different elements ex: CO2 and H2O

Polymers and monomers

molecules that are made up of repeating subunits called monomers, and each monomer is either identical or similar in its chemical structure e.g., carbs contain sugar monomers, nuclei acids contain nucleotide monomers, and proteins contain amino acid monomers

Organic molecules

molecules that contain carbon

Neutralization

neutralizing an acidic solution by adding a base, and vice versa

Hydrophobic interactions

non polar molecules placed in a polar substance (intramolecular)

What substances don't dissolve in water?

non polar molecules, hydrophobic substances that require a carrier protein (e.g., triglycerides, cholesterol)

Intramolecular attraction

occurs between different portions of a large molecule

Suspension

occurs when material that is larger in size than 100 nanometers is mixed with water; doesn't remain mixed together unless it is in motion; opaque or cloudy until the particles drop out of the liquid ex: blood cells within plasma

What is the molecular structure of water?

polar molecule that can form four hydrogen bonds with adjacent water molecules

What substances completely dissolve in water?

polar molecules (e.g., glucose, alcohol)

Protein structure

polymers composed of one or more linear strands of amino acid monomers - 20 different amino acids are normally found in proteins of living organisms - each amino acid has an amine (-NH2) and a carboxylic acid (-COOH) functional group - linked covalently by peptide bonds that are formed during dehydration synthesis

Average atomic mass

protons+neutrons in the atomic nucleus that is shown below the element's symbol

Pyrimidines vs purines

pyrimidines: single ring cytosine (C), uracil (U), and thymine (T) mnemonic: CUT purines: double-ringed adenine (A) and guanine (G)

What substances dissolve and dissociate in water?

salts, ionic compounds, and acids/bases ex: NaCl dissociates in water to form both Na+ and Cl- ions

Fatty acids: saturated, unsaturated, and polysaturated

saturated: lacks double bonds unsaturated: one double bond polysaturated: 2+ double bonds

Chemical compounds

stable associations between two or more elements combined in a fixed ratio (associations classified as either ionic or molecular compounds)

Nuclei acids

store and transfer genetic or hereditary information in cells that ultimately determine the types of proteins synthesized within cells

Ionic compound

structure composed of ions held together in a lattice by ion bonds

Acid

substance that dissociates in water to produce an H+ and an anion; increases the concentration of H+ free in solution; proton donor; pH < 7

Buffer

substance(s) that help to prevent pH change if either excess acid or base is added

Electrolytes

substances that dissolve and dissociate in water, such as salts, acids, and bases; can readily conduct an electric current

Solutes

substances that dissolve in water

Nonelectrolytes

substances that remain intact when introduced to water, such as glucose; does not conduct an electrical current

What determines the concentration of a solution?

the amount of solvent dissolved in a solution

Molecular formula

the chemical constituents of a molecule and their ratios ex: carbonic acid (H2CO3), where the molecule contains two hydrogen atoms, one carbon atom, and three oxygen atoms.

Dehydration synthesis (condensation)

the loss of a water molecule during the formation of complex molecules from simpler components

Temperature

the measure of the kinetic energy, or random movement, of atoms or molecules within a substance

Intermolecular attraction

weak chemical attraction between molecules ex: hydrogen bonds

Solvent

what solutes dissolve in (water)