Biochemical Basics

Question 1

A chemical substance that cannot be broken down further using standard chemical techniques is known as:

Answer 1

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!

Question 2

What is the difference between an atom, a molecule, and a compound?

Answer 2

• 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).

Question 3

Which of the following are contained within the nucleus of a typical atom?

• Protons
• Neutrons
• Electrons

Answer 3

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.

Question 4

Isotopes are atoms with the same number of:

Answer 4

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.

Question 5

Define:

ionic bond

Answer 5

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.

Question 6

Define:

covalent bond

Answer 6

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.

Question 7

What is the chemical formula for water, and is the water molecule polar or nonpolar?

Answer 7

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.

Question 8

How do hydrogen bonds differ from ionic or covalent bonds?

Answer 8

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.

Question 9

Define:

a hydrophilic compound

Answer 9

One that is attracted to water.

Since water is polar, it tends to attract other polar compounds.

Question 10

Define:

a hydrophobic compound

Answer 10

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.

Question 11

Define:

macromolecule

Answer 11

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.

Question 12

Name the four main types of organic macromolecules that are found in living organisms.

Answer 12

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

Carbohydrates are commonly known as sugars, and lipids are commonly known as fats.

Question 13

What is the general chemical formula for a typical carbohydrate?

Answer 13

(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.

Question 14

Define a monosaccharide and give two common examples.

Answer 14

• A carbohydrate that contains only a single sugar subunit.
• Classic examples that you should know for the AP Biology exam are glucose and fructose.

Question 15

Define a disaccharide and give three common examples.

Answer 15

• 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.

Question 16

Define a polysaccharide and give three common examples.

Answer 16

• 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.

Question 17

What type of reaction occurs when two carbohydrate subunits combine to form a disaccharide?

Answer 17

A dehydration reaction.

Dehydration reactions involve the combination (or condensation) of smaller reactants to form a larger product. This occurs along with the loss of a water molecule.

Question 18

What is the molecular formula for glucose?

Answer 18

C₆H₁₂O₆

Remember this formula for the AP Biology exam! Glucose is a six-carbon monosaccharide (meaning that it contains only one sugar subunit).

Question 19

What is the molecular formula for sucrose?

Answer 19

C₁₂H₂₂O₁₁

_{Sucrose is a disaccharide, meaning that it consists of two sugar subunits. Specifically, these subunits are glucose and fructose.}

Question 20

The main component of plant cell walls is classified as which of the four main types of organic macromolecule?

Answer 20

Carbohydrates

Plant cell walls are composed of cellulose, which is a polysaccharide, or carbohydrate polymer.

Question 21

Protein molecules are composed of smaller subunits known as:

Answer 21

Amino acids

Amino acids are the monomers, or individual subunits, that make up protein molecules. Adjacent amino acids are held together by peptide bonds.

Question 22

Which two functional groups are found in all amino acids?

Answer 22

1. amine
2. 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.

Question 23

What functional group is present in all peptide bonds?

Answer 23

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.

Question 24

A laboratory technician is analyzing the composition of a plasma protein. Which elements could he expect to find in this protein’s structure?

Answer 24

• carbon
• hydrogen
• oxygen
• nitrogen

Sulfur also may be present, depending on the particular amino acids in the structure. Some proteins also contain trace amounts of selenium.

Question 25

Which would be expected to have a higher molecular weight: a dipeptide or a polypeptide?

Answer 25

polypeptide

A dipeptide is the smallest form of peptide and contains only two amino acids bound together. Polypeptides typically consist of long strings of amino acids, making them significantly heavier; a polypeptide can include up to around 50 amino acids in total.

Question 26

Name the four levels of protein structure.

Answer 26

• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure

Question 27

Define:

the primary structure of a protein

Answer 27

It is simply its linear amino acid sequence.

Primary structure is often written using either a one- or a three-letter abbreviation for each amino acid (for example, “Gly-Pro-Ile-Cys…” or “GPIC…”).

Question 28

Define:

the secondary structure of a protein

Answer 28

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.

Question 29

Define:

the tertiary structure of a protein

Answer 29

Refers to its large-scale three-dimensional shape.

Tertiary structure is determined by interactions between side chains and by hydrophobic interactions (the tendency for nonpolar groups to avoid facing the watery environment).

Question 30

Define:

the quaternary structure of a protein

Answer 30

It 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.

Question 31

Define:

lipids

Answer 31

A class of organic macromolecule characterized by their nonpolar (non-water-soluble) nature.

Most notably, lipids include triglycerides (fats), oils, steroids, waxes, and phospholipids.

Question 32

What functional groups are present in a typical fatty acid?

Answer 32

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.

Question 33

What type of lipid is pictured here?

Answer 33

triglyceride

A triglyceride is commonly known simply as a fat. It consists of three fatty acid molecules attached to a three-carbon glycerol backbone.

Question 34

The diagram below depicts a fatty acid. Is this fatty acid saturated, monounsaturated, or polyunsaturated?

Answer 34

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.)

Question 35

What type of lipid would be expected to be most predominant in a eukaryotic cell membrane?

Answer 35

phospholipids

The cell membrane (in both eukaryotes and prokaryotes) is composed mainly of phospholipids in the form of a “bilayer,” or double layer.

Question 36

What class of lipid is derived from the molecule below and plays a vital role in the endocrine system?

Answer 36

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.

Question 37

A typical phospholipid includes both a polar “head” region and two nonpolar “tails.” What term describes this property of having both polar and nonpolar regions?

Answer 37

amphipathic

Specifically, the polar “head” region includes phosphate, which is charged; this charge is what gives the head group its polarity. The two “tails” consist of fatty acids, which are largely nonpolar due to their long hydrocarbon chains.

Question 38

Define:

nucleic acids

Answer 38

A class of organic macromolecule, which consists of long chains of nucleotide monomers and are involved in the storage and transmission of genetic material.

The two nucleic acids to know for the AP Biology exam are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Question 39

Structures like that shown below are found in which of the four major classes of organic macromolecules?

Answer 39

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.

Question 40

A student is analyzing an unknown biomolecule. He knows that the molecule includes covalent bonds and that it is not a lipid. He is also certain that the molecule contains carbon, hydrogen, and phosphorus, although it may also include other elements. This biomolecule is most likely a:

Answer 40

Nucleic acid

All four of the main classes of organic macromolecule include covalent bonds, so that piece of information is unhelpful. However, only nucleic acids and (some) lipids can contain phosphorus. Since we are told that this molecule is not a lipid, it must be a nucleic acid.