Chapter 2

Question 1

What are the four major families (types of building blocks) of small organic molecules fundamental to all cells?

Answer 1

1. Fatty acids
2. Amino Acids
3. Sugars (monosaccharides)
4. Nucleotides

Question 2

What type of macromolecule is built from amino acids?

Answer 2

Proteins are built from amino acids

Question 3

What type of macromolecule is built from sugars (monosaccharides)?

Answer 3

Polysaccharides are built from monosaccharides.

Question 4

What type of macromolecule is built from nucleotides?

Answer 4

Nucleic acids are built from nucleotides.

Question 5

What are several functions of Proteins?

Answer 5

• Selecting what molecules cross membranes
• Catalyzing chemical reactions of the metabolic network
• Connecting input signals to output responses (receptors and signal transduction)
• Forming protein filaments for motor proteins to move vesicles and organelles
• Copying and repairing the DNA
• Selecting genes for expression

Question 6

What are several functions of Polysaccharides?

Answer 6

• Provide mechanical support
• Absorb much water protecting cells from drying out
• Serve as storage of energy and organic carbon.

Question 7

What are several functions of Nucleic acids?

Answer 7

• Store genetic information (DNA; deoxyribonucleic acid)
• Involved in gene expression (RNA; ribonucleic acid).
• Copies genes into mRNA (Transcription)
• Uses mRNA copies to direct synthesis of Proteins (Translation)

Question 8

What are the component parts of a phospholipid?

Answer 8

Glycerol + 2 Fatty Acids + a Phosphate Head Group

Question 9

What does it mean to say a molecule is amphipathic?

Answer 9

-Has both a Non-Polar and Polar region.

Question 10

What is a condensation reaction?

Answer 10

-The loss of water (H2O) when a covalent bond forms between two molecules.

Question 11

What is a hydrolysis reaction?

Answer 11

-Water colliding with a covalent bond and breaking the bond to form two molecules: one molecule gains an –OH group, and the other molecule gains a –H.

Question 12

What does it mean to say a protein has a specific sequence?

Answer 12

• A protein is a chain of amino acids. There are 20 different amino acids.
• The order of amino acids in the chain is the sequence.
• The sequence is specific because it is different between different proteins encoded by different genes.

Question 13

What does it mean to say a nucleic acid has a specific sequence?

Answer 13

• A nucleic acid is a chain of nucleotides. There are 4 different nucleotides.
• The order of nucleotides in the chain is the sequence.
• The sequence is specific because it is different between different chunks of DNA, or between RNA copies of different genes.

Question 14

What are three types of noncovalent bonds?

Answer 14

• Ionic bonds: metal + non-metal
• Hydrogen bonds: H + F,O, or N
• van der Waals: lectrons are constantly moving in their orbits. One atom can have excess positive charge and an adjacent atom can have excess negative charge, which results in a slight, very transient attraction to each other.

Question 15

What is the hydrophobic force?

Answer 15

• The hydrophobic force exists because nonpolar molecules (C-C and C-H bonds) disrupt the hydrogen-bonding network of water molecules.
• It is energetically favorable for the nonpolar surfaces to aggregate together to limit nonpolar surface adjacent to water molecules. This reduces the disruption of the hydrogen-bonding network of water molecules.

Question 16

Do any of the four molecules have a portion that has a predominantly nonpolar surface? SEE PICTURE

Answer 16

Yes, the side chain of the amino acid is a nonpolar surface and the tail of the fatty acid is nonpolar.

Question 17

What determines if a protein will bind to a small molecule or another protein?

Answer 17

• To form noncovalent bonds, the surface of the protein and the surface of the partner must have complementarity
• they must fit together so a sufficient area of their surfaces are pushing into each other and charge distribution must match - positive across from negative, or no charge across from no charge.

Question 18

What determines how long the two partners stay stuck together?

Answer 18

• The number of noncovalent bonds at the interface between the two molecules.
• Two molecules that form noncovalent bonds are said to have affinity for each other.

Question 19

When a protein binds to a partner, the binding is because of noncovalent bonds that form at the interface between the two partners.

In what way would the interaction be changed if covalent bonds, instead of noncovalent bonds, formed at the interface?

Answer 19

Noncovalent bonds are much weaker than covalent bonds. The weakness makes noncovalent bonds transient relative to covalent bonds.

• Noncovalent bonds can be broken by thermal motion.
• Noncovalent bonds, however, add up so binding can last for a range of time depending on the number of noncovalent bonds.
• Covalent bonds are stronger than noncovalent bonds. More energy than that supplied by thermal motion is needed to break a covalent bond.
• If a covalent bond formed at the interface, the two partners would remain attached for a much longer time relative to noncovalent bonds.
• Covalent bonds at interfaces would make interactions less dynamic. In a cell, binding of two partners (substrate and enzyme, for example) often needs to be very transient.

Question 20

How many electrons would atoms of the elements listed below preferentially gain or lose in order to obtain a filled outer electron shell? For each element, does the element achieve a filled outer electron shell be sharing electrons (forming a covalent bond) or by undergoing an oxidation-reduction reaction?

Hydrogen

Carbon

Nitrogen

Oxygen

Sodium

Potassium

Calcium

Answer 20

Hydrogen Gain or lose one electron. Gain an electron by forming a covalent bond, or lose an electron by oxidation.

Carbon Gain four electrons by forming covalent bonds.

Nitrogen Gain three electrons by forming covalent bonds.

Oxygen Gain two electrons by forming covalent bonds.

Sodium Lose one electron by oxidation.

Potassium Lose one electron by oxidation.

Calcium Lose two electrons by oxidation.

Question 21

What mechanisms do proteins use to achieve their functions?

Answer 21

The proteins achieve their functions by three fundamental mechanisms:
-selective binding

• catalysis(rate of reactions)
• coupling (allostery)(change shape).

Question 22

Is a non-polar region hydrophobic? What does it cause?

Answer 22

The nonpolar region is hydrophobic, and it is energetically favorable to minimize its surface that is exposed to water.

Question 23

Is a polar region hydrophilic? What does this bond to?

Answer 23

The polar region is hydrophilic, and it is favorable to maximize its surface that is exposed to water. The polar region will form noncovalent bonds with water.

Question 24

Are macromolecules polymers?

Answer 24

Yes.
-Macromolecules are formed by the sequential addition of monomers to a growing chain.

• The monomers, or subunits, are chemically related to each other, if not identical.
• “Poly” means many units, so macromolecules are polymers: many monomers covalently linked together into a chain.

Note: Phospholipids are an exception. A phospholipid consists of two fatty acids linked to a glycerol linked to a phosphate, which may have additional modifications. A lipid bilayer made up of phospholipids is NOT a macromolecule, because the phospholipids are NOT covalently linked to each other.

Question 25

What polymer is a protein for?

Answer 25

A protein is a polymer of amino acids (20 different amino acids).

Question 26

What polymer is a nucleic acid for?

Answer 26

Nucleic acid is a polymer of nucleotides DNA adenosine, guanosine, cytosine, and thymidine RNA adenosine, guanosine, cytosine, and uridine

Question 27

What polymer is a polysaccharide for?

Answer 27

Polysaccharide is a polymer of monosaccharides (glucose for glycogen and starch; but also many different monosaccharides)

Question 28

True or False? Proteins are so remarkably diverse because each is made from a unique mixture of amino acids that are linked in random order.

Answer 28

Proteins are so remarkably diverse because each is made from a unique mixture of amino acids that are linked in random order. - FALSE - Random linking of amino acids is NOT how proteins are made. - The order (sequence) of a particular protein is determined by the DNA sequence (and more directly, the sequence of the RNA copy) that codes for the protein.

Question 29

True or False? | Lipid bilayers are macromolecules that are made up mostly of phospholipid subunits.

Answer 29

Lipid bilayers are macromolecules that are made up mostly of phospholipid subunits. - FALSE - Lipid bilayers are NOT macromolecules. - Lipid bilayers are made up of millions of individual phospholipid subunits that are NOT connected by covalent bonds.

Question 30

True or False? | Nucleic acids contain sugar groups.

Answer 30

Nucleic acids contain sugar groups. - TRUE - Nucleic acids are a chain of nucleotides. - A nucleotide consists of a nitrogenous base, a sugar and a phosphate.

Question 31

True or False? Hydrogen bonds are weak and can be broken by thermal energy, yet they contribute significantly to the selectivity of interactions between macromolecules.

Answer 31

Hydrogen bonds are weak and can be broken by thermal energy, yet they contribute significantly to the selectivity of interactions between macromolecules. - TRUE - Although a single hydrogen bond is weak, many hydrogen bonds often form between interacting macromolecules. - The hydrogen bonds collectively can prevent thermal energy from immediately disrupting the interaction.

Question 32

True or False? | The hydrophobic tails of phospholipid molecules form noncovalent bonds with water.

Answer 32

The hydrophobic tails of phospholipid molecules form noncovalent bonds with water. - True - It is the mutual repulsion to water that makes the aggregation of phospholipid tails into a bilayer energetically favorable.

Question 33

True or False? | DNA contains the four different bases A, G, U and C.

Answer 33

DNA contains the four different bases A, G, U and C. - FALSE - DNA contains thymidine, not uridine.

Question 34

How do covalent bonds affect geometry (shape)?

Answer 34

- Covalent bonds determine the geometry (shape) of the molecule - The spatial arrangement of the molecule’s atoms and the direction an atom stands out from the backbone of the molecule.

Question 35

How do covalent bonds affect the flexibility of a molecule?

Answer 35

- Covalent bonds determine the flexibility of a molecule. - In the case of a single covalent bond, the two atoms are free to rotate. - Double and triple bonds, as well as single bonds that unite atoms in a ring, prevent rotation of the joined atoms, hence reducing flexibility.

Question 36

How do covalent bond affect polarity of a molecule?

Answer 36

- Covalent bonds determine polarity. - If one of the atoms pulls the shared electrons closer to its atomic nucleus then that atom will have excess negative charge and the other atom will have excess positive charge.

Question 37

How does having excess charge on a polar molecule affect its hydrogen bonding?

Answer 37

- Excess charge allows for hydrogen bonding: electropositive H is attracted to electronegative O or N on other molecules resulting in a hydrogen bond between the two molecules. - Hydrogen bonds between polar molecules and polar molecules results in the polar molecule being dissolved in the water and having a hydrogen shell: a layer of water molecules surrounding the polar groups of the molecule. Excess charge also makes the covalent bond more reactive, which means that less energy (activation energy) has to be put into breaking the covalent bond.

Question 38

How do van der Waals attractions affect the lipid bilayer?

Answer 38

When many nonpolar atoms are crowded up against each other, then the many weak van der Waals attractions add up and reduce fluidity (lipid bilayer) or increase stability (protein interior)

Question 39

Label and draw the following structures: a lipid, a sugar, an amino acid or a nucleotide.

Answer 39

See drawing!

Question 40

List three different covalent bonds that are polar, and two different covalent bonds that are nonpolar

Answer 40

Polar: C-O, O-H, C-N, N-H Nonpolar: C-C, C-H

Question 41

Describe the properties of Sugar in terms of flexibility, chemical polarity and opportunities for forming non covalent bonds with a partner.

Answer 41

See Q. 12 Flexibility: The covalent bonds of the sugar ring cannot rotate, so the molecule is rigid in the plane of the ring. The atoms attached to the ring atoms either project above or below the ring, but cannot switch due to the rigid ring. The groups (-OH and -CH2OH) projecting above or below the ring, however, can rotate. Polarity: The groups (-OH and -CH2OH) projecting above or below the ring, however, can rotate. The numerous hydroxyl (-OH) groups have chemical polarity: excess negative charge on the oxygen and excess positive charge on the hydrogen. Opportunities for non-covalent bonds: The polar groups provide opportunity for hydrogen bonds.

Question 42

Describe the properties of Fatty Acids in terms of flexibility, chemical polarity and opportunities for forming non covalent bonds with a partner.

Answer 42

Flexibility: All the single covalent bonds of the fatty acid are free to rotate, so the molecule is flexible, although all the atoms projecting off the carbon backbone are the same: hydrogens. The carboxylic acid (-COO-) is free to rotate. Polarity: The carboxylic acid has a full-negative charge as well as excess negative charge on oxygen and excess positive charge on the attached carbon. However, the -C-H tail is nonpolar. Opportunities for non-covalent bonds: The full-charge provides opportunity for an ionic bond, while the excess negative charge could be involved in a hydrogen bond. The nonpolar tail will favorably aggregate with other nonpolar surfaces, at which point there is opportunity for many van der Waals attractions.

Question 43

Describe the properties of Amino Acids in terms of flexibility, chemical polarity and opportunities for forming non covalent bonds with a partner.

Answer 43

Flexibility: The side chain of the amino acid is a ring. The atoms of the ring cannot rotate, so all remain in a single plane. However, the covalent bond between the ring and the carbon can rotate, so the ring can rotate relative to the rest of the molecule. Similarly the amine (-NH2) and the carboxylic acid (-COOH) can rotate, so overall the amino acid is quite flexible. Polarity: The nitrogen and oxygen have excess negative charge, and the attached hydrogens have excess positive charge, so there are opportunities for hydrogen bonding. The side chain is nonpolar, so would favorably aggregate with other nonpolar surfaces, at which point there is opportunity for many van der Waals attractions. Opportunities for non-covalent bonds:

Question 44

Describe the properties of Nucleotides in terms of flexibility, chemical polarity and opportunities for forming non covalent bonds with a partner.

Answer 44

Flexibility: The nitrogenous base and the sugar are both ring structures, so the atoms within the rings cannot rotate and remain in a single plane. However, the covalent bond between the sugar and nitrogenous base can rotate, so the two rings can rotate relative to each other, so the nucleotide is quite flexible. Likewise, the triphosphate can rotate relative to the sugar ring. Polarity: The triphosphate has much excess negative charge on the oxygens as well as full negative charges. The -OH of the sugar are also polar, with excess negative on the oxygen and excess positive on the hydrogen. The nitrogens within the ring of the nitrogenous base, and the amine (-NH2) nitrogen have excess negative charge, while the amine hydrogens have excess positive charge. Opportunities for non-covalent bonds: The full negative charges provide opportunity for ionic bonds, while the excess charges on nitrogen, oxygen and hydrogen provide opportunity for hydrogen bonds.