Biology: Atomic Structure, Chemical Bonds, and Organic Molecules

Element

a pure substance that cannot be created or broken down by ordinary chemical means.

Compound

two or more elements join to make a new substance.

Atom

smallest quantity of an element.

Atomic Number

Based on the number of protons in the nucleus.

Atomic Mass

Counts both protons and neutrons (Usually a 1:1 ratio).

Isotopes

various number of neutrons in the nucleus.

Elements that make up 95% of the human body

Hydrogen, Nitrogen, Oxygen, Carbon

Radioactive isotopes

Unstable, heavy isotope that gives off subatomic particles, or electromagnetic energy, as it decays; also called radioisotopes. Are often used in the medical field.

The number of electrons in Valence shell

The factor that most strongly governs the tendency of an atom to

participate in chemical reactions

Ions

Atoms in which the number of protons and electrons differ.

Cations

Contain more protons than electrons and have a POSITIVE (+) charge.

Anions

Contain fewer protons than electrons and have a NEGATIVE (-) charge.

Oxidation

Loss of electrons.

Reduction

Gain of electrons.

Chemical bonds

Electrical attractions that hold atoms in the same vicinity.

Molecule

stable grouping of two or more atoms held together by a chemical bond.

Ionic Bonds

ongoing close association between ions of opposite charge.

Covalent Bonds

two atoms share electron pairs to fill their valence shell for stability.

Hydrogen Bonds

slight positive of Hydrogen is attracted to the slightly negative aspect of another molecule.

Chemical reaction

occurs during the formation or breaking of chemical bonds.

Decomposition reaction

(catabolism): AB --> A+B.

Synthesis reaction

(anabolism): A+B --> AB.

Exchange reaction

(reversible): AB <--> A+B. type of chemical reaction in which bonds are both formed and broken, resulting in the transfer of components

Activation energy

gets a reaction started.

Exergonic Reaction

Produce more energy than they use.

Endergonic Reactions

Consume more energy than they produce.

Reactants

materials going into a reaction.

Products

materials coming out of a reaction.

Enzymes

proteins that lower the amount of activation energy needed.

Organic Molecules

Compounds based on Carbon and Hydrogen.

Inorganic Molecules

NOT based on carbon and hydrogen.

Water

Universal Solvent, 70% of adult body weight. “Heat Sink” Transfer heat around the body. Necessary for many chemical reactions

Hydrophilic

Attracted to water, polar.

Hydrophobic

Not attracted to water, nonpolar.

Dehydration Synthesis

Formation of larger molecules from smaller reactants, accompanied by the loss of a water molecule.

Hydrolysis

Water molecule is added to a larger molecule, causing it to break down into smaller components.

Acids

dissolve to release a hydrogen ION (H+) (aka proton).

Strong Acid

release ALL of their H+ into solution (ex: HCL).

Weak Acid

do not ionize completely (ex: vinegar).

Bases

dissolve to release a hydroxide ion (OH-).

Strong Base

release ALL of their OH- into solution -OR- accept large quantities of (H+) to create water (ex: NaOH).

Weak Base

do not ionize completely -OR- accept small quantities of (H+) to create water (ex: HCO3-).

Buffer

Solution of a weak acid and its conjugate base. It opposes wide fluctuations in the pH of body fluids

pH

Scale of measuring acidity or alkalinity

pH Range

0-14 (the more basic (alkaline) the higher the pH) (the more acidic, the lower the pH)

Chemically neutral

pH 7

Blood pH Range

7.35-7.45 (slightly alkaline)

Urine pH range

4.5-8.0 (wide range of possibility)

Stomach pH

1.5-3.5

Functional Group

a group of atoms bonded together so strongly that they tend to act as a single unit

Inorganic substances

Water, Salts, Acids/Bases

Organic substances

Carbohydrates, Lipids, Proteins, Nucleic Acids, High Energy Compounds. All organic molecules are based on a core of carbon

Carbohydrates

Class of organic compounds built from sugars, molecules containing carbon, hydrogen, and oxygen in a 1-2-1 ratio. Categorized by number of monomers (single units) They're quick energy sources and may be used as components of cell membrane.

Monosaccharides

simple sugars (1 carbon-based ring each) (carbohydrates)

Disaccharides

2 simple sugars condensed by dehydration synthesis (carbohydrates)

Polysaccharides

chains of many simple sugars

5 important monosaccharides

Glucose, Fructose, Galactose, Deoxyribose, Ribose

3 important polysaccharides

Starches, Glycogen, Fiber

Lipids

mainly hydrophobic molecules made mostly of carbon and hydrogen. Examples: fats, oils, waxes

Fatty Acids

Long chains of carbon and hydrogen that end in a carboxyl group.

Saturated (fatty acid)

no double bonds; contain the max number of hydrogens; Shape is straight; Pack together tightly to be solid at room temp: lard, butter, etc.

Unsaturated (fatty acid)

contain double bonds between carbons which cause the structure to "kink"; Cannot pack together tightly; thus, liquid at room temperature

Triglycerides

One of the most common dietary lipids. Most abundant lipid in body tissues. Lipid compound composed of a glycerol molecule bonded with 3 fatty acid chains

Phospholipids

Have hydrophilic heads and hydrophobic tails; Structural lipids: cell membranes

Sterols/Steroids

Ring-shaped lipids; The basis for cholesterols, many hormones, and more

Prostaglandins

Lipid compound derived from fatty acid chains and important in regulating several body processes. The broader category is "eicosanoids" which includes leukotrienes; Prostaglandins help mediate blood pressure and inflammation; Leukotrienes function in the immune system

Proteins

the most abundant organic molecule in the body and all contain nitrogen.

Amino acids

the building blocks of proteins. There are 20 different amino acids.

Peptide Bonds

The bonds between amino acids

Functions of Proteins

Support: structural proteins; Movement: contractile proteins; Transport: Transport proteins; Buffering: regulation of pH; Metabolic regulation: enzymes; Coordination and control: hormones; Defense: antibodies and other immune proteins

Primary structure protein

Sequence of amino acids in a polypeptide chain (straight)

Secondary structure protein

Can be an alpha helix (zigzag) or beta-pleated sheet. Maintained by hydrogen bonds between amino acids in different regions of the original polypeptide strand

Tertiary structure protein

occurs as a result of further folding and bonding of the secondary structure. (Curling up into a little ball)

Quaternary structure

result of interactions between two or more tertiary subunits. (Big curled ball)

Protein Function

Based on shape

Protein Shape

Based on sequence of amino acids

Denaturation

Loss of shape and function due to heat or pH

Fibrous Protein Shape

Structural sheets or strands

Globular Proteins Shape

Soluble spheres with active functions

Substrates

bind to the enzyme during enzymatic reactions and react with one another

Active sites

locations on the enzyme that fit a certain substrate

Nucleic Acids

large, organic molecules in the cell nucleus which store and process information at the molecular level.

Deoxyribonucleic Acid (DNA)

Determines inherited characteristics. Directs protein synthesis. Controls enzyme production. Controls metabolism

Ribonucleic Acid (RNA)

Codes intermediate steps in protein synthesis

Nucleotides

Building blocks are one or more phosphate groups, a pentose sugar, and nitrogen-containing base

Adenine (A) pairs with

Thymine (T)

Guanine (G) pairs with

Cytosine (C)

RNA uses what instead of Thymine?

Uracil (U)

Adenosine Triphosphate (ATP)

This is the main energy model for human life.

ATP

3 phosphates/Adenosine Triphosphate

ADP

2 phosphates/Adenosine Diphosphate

AMP

1 phosphate/Adenosine Monophosphate

Chemical reactions can be influenced by?

Temperature, molecule size, concentration of reactants and products, catalysts.

Bond

Electrical force linking atoms

Catalyst

Substance that increases the rate of a chemical reaction without itself being changed in the process

Colloid

Liquid mixture in which the solute particles consist of clumps of molecules large enough to scatter light

Disulfide Bond

Covalent bond formed within a polypeptide between sulfide groups of sulfur-containing amino acids, for example, cysteine

Electron

Subatomic particle having a negative charge and nearly no mass; found orbiting the atom’s nucleus

Electron Shell

Area of space a given distance from an atom’s nucleus in which electrons are grouped