Biochemical Basics Flashcards
A chemical substance that cannot be broken down further using standard chemical techniques is known as:
An element
For example, carbon (C) is an element. Atoms of a particular element always have the same number of protons. For example, all carbon atoms have 6 protons!
What is the difference between an atom, a molecule, and a compound?
An atom is the fundamental unit of matter. Atoms contain protons, neutrons, and electrons.
A molecule is a group of two or more atoms, connected by chemical bonds (for example, O2).
A compound is a molecule that contains atoms of more than one element (for example, H2O).
Which of the following are contained within the nucleus of a typical atom?
- Protons
- Neutrons
- Electrons
A typical atomic nucleus contains protons and neutrons. Electrons are not found in the nucleus; instead, they are located in regions (“shells”) surrounding the nucleus.
For the AP Biology exam, remember that a proton has a positive charge, while an electron has an equivalent negative charge. Neutrons are neutral, meaning that they are uncharged.
Isotopes are atoms with the same number of:
Protons
Isotopes are atoms with the same number of protons, meaning that they must represent the same element. Isotopes differ in their number of neutrons.
Define:
an ionic bond
An ionic bond is a chemical bond that forms due to the complete transfer of electrons from one atom to another.
The atom that gains electrons is given a negative charge, while the atom that gives up electrons is given a positive charge.
Define:
a covalent bond
A covalent bond is a chemical bond that forms via the sharing (not complete transfer) of electrons.
When the electrons are shared unequally, the bond is polar covalent. For example, H2O contains two polar covalent bonds between H and O, because these atoms have different electronegativities (attraction to electrons in a bond).
When the electrons are shared equally, the bond is nonpolar covalent. For example, O2 contains a nonpolar covalent bond between the two O atoms, which have the same electronegativity.
What is the chemical formula for water, and is the water molecule polar or nonpolar?
Water has a formula of H2O, and it is polar.
The water molecule (shown here) is bent due to the presence of two lone pairs on the central oxygen atom. Oxygen is more electronegative than hydrogen, so the oxygen atom will carry a partial negative charge, while the hydrogen atoms will be partially positive. Molecules with asymmetrical charge distributions like this one are polar.
How do hydrogen bonds differ from ionic or covalent bonds?
Hydrogen bonds are intermolecular, which means they occur between two or more different molecules. Ionic and covalent bonds are intramolecular, meaning they connect atoms within a single molecule.
Hydrogen bonds are attractive forces. For the AP Biology exam, be sure to remember that water molecules can hydrogen bond with each other.
Define:
a hydrophilic compound
A hydrophilic compound is one that is attracted to water.
Since water is polar, it tends to attract other polar compounds.
Define:
a hydrophobic compound
A hydrophobic compound is one that is repelled by water.
Since water is polar, it tends to repel nonpolar compounds. A classic example is an oil slick on the top of the ocean. Oil is nonpolar, so it is not attracted to the ocean water, and the two liquids do not mix.
Define:
a macromolecule
A macromolecule is a molecule that contains an extremely large number of atoms.
For the AP Biology exam, most macromolecules you need to know are polymers, or long chains of smaller subunits.
Name the four main types of organic macromolecules that are found in living organisms.
Carbohydrates, lipids, proteins, and nucleic acids
Carbohydrates are commonly known as sugars, and lipids are commonly known as fats.
What is the general chemical formula for a typical carbohydrate?
A typical carbohydrate has a chemical formula of (CH2O)n, where n is an integer.
This can be easily remembered, since H2O represents water. Carbohydrates are simply “hydrated carbons.” Note that a few rare carbohydrates, like deoxyribose, have formulas that differ from this rule.
Define a monosaccharide and give two common examples.
A monosaccharide is a carbohydrate that contains only a single sugar subunit.
Classic examples that you should know for the AP Biology exam are glucose and fructose.
Define a disaccharide and give three common examples.
A disaccharide is a carbohydrate that consists of two sugar subunits, joined by a bond called a glycosidic linkage.
Classic examples that you should know for the AP Biology exam are maltose, lactose, and sucrose.
Define a polysaccharide and give three common examples.
A polysaccharide is a carbohydrate that consists of a polymer (or long chain) of many sugar subunits.
Classic examples that you should know for the AP Biology exam are glycogen, starch, and cellulose.
Which two functional groups are found in all amino acids?
An amino acid must contain an amine and a carboxylic acid. Each amino acid also contains a specific side chain.
The amino acids that you may see on the AP Biology exam are alpha amino acids, meaning that the amine group, the side chain, and the carboxylic acid are all attached to the same central carbon.
What functional group is present in all peptide bonds?
Peptide bonds contain amides. In fact, they are sometimes alternatively known as amide linkages.
A peptide bond forms when the amine group of one amino acid attacks the carbonyl carbon of another.
Define:
the secondary structure of a protein
The secondary structure of a protein refers to the folding of the amino acid chain into repetitive structures due to hydrogen bonding between backbone groups.
Two forms of secondary structure that you should remember for the AP Biology exam are alpha helices and beta-pleated sheets. The partial structure of a beta-pleated sheet is shown here.
Define:
the quaternary structure of a protein
Quaternary protein structure is present only in proteins that are composed of multiple subunits. This level of structure refers to interactions between subunits.
For example, hemoglobin (shown here) consists of four separate subunits, held together by various interactions and attractive forces.
What functional groups are present in a typical fatty acid?
A fatty acid includes a carboxylic acid (COOH) group attached to a hydrocarbon chain.
Fatty acids can combine with glycerol to form triglycerides, or fat. Fatty acids can also be broken down to provide cells with energy.
What type of lipid is pictured here?
The lipid pictured here is a triglyceride, commonly known simply as a fat.
A triglyceride consists of three fatty acid molecules attached to a three-carbon glycerol backbone.
The diagram below depicts a fatty acid. Is this fatty acid saturated, monounsaturated, or polyunsaturated?
This fatty acid is polyunsaturated.
Saturated fatty acids have carbon chains that include only single bonds, while unsaturated fatty acids include one or more double bonds in their chains. Since this fatty acid contains three carbon-carbon double bonds, it is polyunsaturated. (To be monounsaturated, a fatty acid must include only one double bond in its carbon chain.)
What class of lipid is derived from the molecule below and plays a vital role in the endocrine system?
Steroid hormones
Steroid hormones are derived from cholesterol (shown here). These lipid molecules can be easily spotted due to their structures, which include four fused rings.
Structures like that shown below are found in which of the four major classes of organic macromolecules?
Nucleic acids
The structure pictured here is a nucleotide, as is evident from its nitrogenous base, sugar, and phosphate group. Nucleotides are the monomers (“building blocks”) that form nucleic acids, including DNA and RNA.
