Key Concepts in Chemistry and Biomolecules

Atom

An atom is the smallest unit of an element and are composed of subatomic particles.

Element

An atom that has a specific number of protons. For example: 6 protons is always carbon and 8 protons is always Oxygen.

Molecules

Molecules are two or more atoms bonded together.

O2

A diatomic molecule consisting of two oxygen atoms.

Isomers

Molecules with identical formulas but different atomic arrangements.

Compound

A molecule which has two or more elements.

Chemical formula

Atomic makeup of molecules; elements and how many atoms of each are present.

Neutron

Subatomic particles with no charge.

Proton

A positively charged subatomic particle.

Atomic number

The number for protons in each atom.

Atomic mass

The sum of protons and neutrons.

Electron

A negatively charged subatomic particle.

Electron shells

Surround the nucleus holding the electrons, keeping them close to the neutrons.

Nucleus

The center of the atom, containing protons and neutrons.

Orbital

Region surrounding the nucleus, occupied by electrons.

Chemical Bonding

The force that holds atoms or ions together to form molecules.

Ionic Bond

The actual transfer of an electron between atoms results in an attraction.

Cations

Atoms that lose electrons and become positively charged.

Anions

Atoms that gain electrons and become negatively charged.

Covalent Bonds

Atoms share electrons between them; harder to break.

Hydrogen Bonds

Weak bond between a partial positive/negative charge in two particles.

Ion

An atom or molecule with an electrical charge, resulting from gain or loss of one or more electrons.

Isotope

Atoms of an element which differ in their neutron number.

Valence Shell

The outermost occupied shell; the number of electrons in the valence shell determines reactivity with other atoms.

Polar

A molecule where the electrical charge is being distributed unevenly across the molecule.

Nonpolar

A molecule where the electrical charge is being distributed evenly along the molecule.

Hydrophobic

Repel water or fail to mix with water.

Hydrophilic

Attracted to water molecules and tends to dissolve and mix with water.

Cohesion

The attraction between the molecules of the same substance.

Adhesion

The attraction between the molecules of different substances.

Solution

Composed of solvent which are the most abundant component and solute which dissolves in the solvent.

Buffer

Compounds that prevent pH changes (balance/finetune the pH).

Organic

Contain carbon atoms; most all carbon molecules are considered organic.

Carbon Backbone

Largely based on chains of carbon atoms.

Functional Group

Are reactive structures, involving reactive atoms in various arrangements that are bonded to the carbon backbone, able to modify the reactivity and polarity.

Macromolecule

Polymers consisting of many small repeating molecules called monomers, consist of the biomolecules.

Monomer

Join by dehydration synthesis to form macromolecules.

Polymer

Small organic molecules can combine into large macromolecules.

Dehydration Reaction

Dehydration of an alcohol to produce an alkene and a water.

Synthesis Reaction

A chemical reaction that combines 2 or more substances to create a complex product.

Anabolism

The synthesis of molecules in a cell; to add things together is larger and more complex molecules.

Decomposition Reactions

Molecules splitting into smaller molecules, ions, atoms.

Catabolism

All decomposition reactions in a cell.

Hydrolysis reaction

Water is used to break down a larger molecule- through displacing organic bonds.

Exchange Reactions

Bonds form and break out but complexity is unchanged-molecules move around.

Reversing Chemical Reactions

Most chemical reactions can go in either direction.

Carbohydrate

Molecules made of carbon, hydrogen and oxygen. Typically 1:2:1 ratio.

Monosaccharide

Monomers of carbohydrates, simple sugars with three to seven carbon atoms.

Polysaccharide

Consist of ten or hundreds of monosaccharides bonded together.

Lipid

A family of hydrocarbon compounds. These tend to be hydrophobic and not dissolving in water.

Fat

Triglycerides which contain glycerol and fatty acids formed by dehydration synthesis.

Saturated

No double bonds in the fatty acids, solid at room temperature.

Unsaturated

One or more double bonds in the fatty acids, atoms packed more together making it liquid at room temperature.

Complex Lipids

Includes Carbon, Hydrogen, + Phosphate, Nitrogen, and/or Sulfur.

Protein

Amino acid polymers which consist of Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur.

Flagella

Have flagella to be able to move around.

Bacterial Toxins

Have some bacterial toxins.

Protein Structure

Four levels: Primary, Secondary, Tertiary, Quaternary.

Primary Structure

Amino acid sequence (dictated by gene sequence).

Secondary Structure

Hydrogen bonding between peptide backbone.

Tertiary Structure

Folding and bonding with R groups.

Quaternary Structure

Multiple polypeptides to form a large functional unit.

Amino Acid

There are 20 different types of amino acids found in organisms.

Amino Acid Structure

Structure consists of Central Carbon, Amino group -NH2, Acidic group -COOH, and a radical (R) group that varies with each amino acid.

R Groups

R groups vary in size, affinities, binding properties, polar/nonpolar, charged or neutral.

Peptide Bond

Bonds amino acids together creating proteins, this formation is called dehydration reaction.

Hydrolysis Reaction

Breaking the peptide bond is therefore a hydrolysis reaction.

Enzyme

A biological catalyst and is almost always a protein.

Denature

Denaturation is the process in which proteins or DNA lose their quaternary structure.

Nucleic Acid

Include both DNA and RNA (polymers of nucleotides).

DNA

Deoxyribonucleic acid which contains deoxyribose, is a double helix, and used for storage.

RNA

Ribonucleic acid, contains ribose, is a single stranded, useful for facilitating a couple of types of chemical reactions.

Nucleotide

Phosphate groups, A pentose sugar, A nitrogenous base.

Properties of Atoms

Know the charges, weights and locations of Protons, Neutrons and Electrons.

Bohr Model

Understand the Bohr model of the atom (nucleus in center with electron orbitals surrounding).

Chemical Bonds

Ionic bonds involve electron donation from one atom to another.

Covalent Bonds

Covalent bonds involve sharing of electrons by merging valence orbitals.

Hydrogen Bonds

Hydrogen bonds form between slight charges on two different molecules; form a weak, temporary interaction.

Water Chemistry

Water is polar, the hydrogens are positive and the oxygen negative.

pH

Water can become ionized into H+ and OH-. Molecules which increase H+ in a solution are acids, those that reduce H+ are bases.

H2O

HO- (hydroxide ion) + H+ (hydrogen ion)

pH

A measure of the hydrogen ion concentration in a solution.

Acidic pH

More H+ lower pH.

Basic pH

Less H+ higher pH.

Neutral pH

Pure water is defined as the neutral pH.

pH Scale

[0 -- Acid < pH 7 = Neutral < Basic (Alkaline) -- 14]

Buffers

Molecules which resist pH change, by absorbing H+ in acidic solutions or releasing H+ in basic solutions.

Organic Chemistry

Refers to chemistry involving carbon (usually carbon-carbon bonds).

Carbon

Has 6 protons; therefore, it typically has 6 electrons (4 valence), which means it makes 4 bonds.

Polymerization Reactions

Typically dehydration reactions where an (OH) group from one monomer is joined to a (H) group from another monomer and water is released.

Hydrolysis Reactions

Break bonds by introducing a water molecule between the two atoms.

Polysaccharides

Polymers of monosaccharides.

Carbohydrates

Polysaccharides are polymers of monosaccharides.

Proteins

Polypeptides are polymers of amino acids.

Nucleic Acids

DNA and RNA are polymers of nucleotides.

Lipids

Mainly carbon and hydrogen (non-polar) so they tend to be hydrophobic.

Simple Sugars

Monosaccharides can consist of 6 (hexose) or 5 (pentose) carbon molecules.

Disaccharides

Consist of 2 monosaccharides bonded together.

Fatty Acids

Long chains of carbon and hydrogen.

Saturated Fatty Acids

No double bonds exist.