Ch 5: Structure and Function of Biological Molecules

Question 1

What are the four major classes of macromolecules?

Answer 1

The four major classes of macromolecules are carbohydrates, proteins, nucleic acids, and lipids. Carbohydrates are macromolecules that provide structure and energy. Proteins have many functions, which include repairing cells, transporting nutrients, and catalyzing reactions. Nucleic acids contain genetic information. Lipids provide energy, make up cell membranes, and act as hormones.

Question 2

Define the terms polymer and monomer.

Answer 2

A monomer is a single molecule and many of them make up the building blocks of polymers. Polymers are long chains of monomers linked together, composed of many similar or identical molecules.

Question 3

A dehydration reaction is the process to connect monomers together. Explain how this process works and the role of water.

Answer 3

A dehydration reaction removes a hydroxyl group (-OH) and a hydrogen (-H) atom from each of the reactants, resulting in an extra water molecule. The remaining hydrogen and hydroxyl group of the monomers are attracted and link together to connect the monomers together.

Question 4

What does the term “hydrolysis” refer to? Explain.

Answer 4

Hydrolysis is the reverse of a dehydration reaction. “Hydro” means water, and “lysis” means to split or separate, so a hydrolysis reaction uses a water molecule to break down the covalent bonds between two monomers. A water molecule contributes a hydroxyl group or a hydrogen to one of the two reactants, which severs their covalent bond.

Question 5

There are thousands of different kinds of macromolecules and it is this diversity that makes cells, siblings, strangers, and species different from each other. Explain how this diversity could exist given that there are a very limited number of monomers (only 40-50!).

Answer 5

A very limited number of monomers can result in a variety of macromolecules due to arrangement, similar to how 26 letters in the alphabet make up the entire English language. Different combinations of monomers can produce different macromolecules.

Question 6

Explain the meaning, sources of diversity for simple sugars, and important functions of monosaccharides.

Answer 6

“Mono” meaning one and “saccharide” meaning sugar. When put together, a monosaccharide is a single sugar molecule. The molecular formulas of monosaccharides typically contain some multiple of CH2O. They each have a carbonyl group and multiple hydroxyl groups. Depending on the location of the carbonyl group, monosaccharides can be aldose or ketose. Simple sugars can be extremely diverse through the arrangement around asymmetric carbons, where the carbonyl group is located, and the length of their carbon skeletons. Monosaccharides are major nutrients for cells, and their carbon skeletons can be used to create other organic molecules.

Question 7

What is a disaccharide? What is a “glycosidic linkage” and how is it involved?

Answer 7

A disaccharide is a sugar molecule consisting of two monosaccharides. A glycosidic linkage is the bond between two monosaccharides (formed by a dehydration reaction) to form a disaccharide. In order for organisms to get energy, they must break down the glycosidic linkages between monosaccharides.

Question 8

A dehydration reaction joins two glucose molecules to form maltose. The formula for glucose is C6H12O6. What is the formula for maltose?

Answer 8

C6H12O6 + C6H12O6 → C12H22O11 (Maltose)

Question 9

Starch and glycogen are both polysaccharides comprised entirely of glucose monomers. Compare and contrast these two polysaccharides.

Answer 9

Starch is a polymer of glucose monomers, and synthesizing starch enables the plant to stockpile extra glucose. Starch can be hydrolyzed by plants to withdraw its stored energy. Like starch, glycogen also stores energy. However, starches are unbranched or somewhat branched, while glycogen is extensively branched, making more free ends available for animals to break down for energy

Question 10

Cellulose is a structural polysaccharide.

• — How is it different from starch?
• — What is the purpose of cellulose? What does it do for a plant?

Answer 10

Cellulose is a structural polysaccharide. Unlike starch, which is a storage polysaccharide, cellulose does not provide energy. The structure of both polysaccharides are different due to slightly differing glycosidic linkages (but both are polymers of glucose with 1-4 linkages), where cellulose is long and branched out. Due to the many layers and branches of cellulose, it makes for a good barrier for plant cell walls, which help protect the contents of plant cells.

Question 11

Lipids are not polymers and they are the most diverse class of macromolecules. What do they all have in common?

Answer 11

All compounds classified as lipids do not mix well with water, or are hydrophobic. Lipids are made up of hydrocarbon regions with relatively non polar C-H bonds.

Question 12

What are the smaller molecules that make up a fat? What type of reaction is used to join the smaller molecules together?

Answer 12

A glycerol (an alcohol where each carbon atom is attached to a hydroxyl group) and three fatty acids make up a fat, joined together by dehydration reactions.

Question 13

What is “atherosclerosis”? Explain what happens in this condition.
—- Which type of “fats” contribute most significantly to this condition?

Answer 13

Saturated fats contribute most to atherosclerosis, a condition where plaques develop within blood vessels and cause them to bulge inward, interfering with blood flow and resilience of the vessel.

Question 14

List and describe 3 very important functions of fat.

Answer 14

Fats provide stored energy, and release a high amount. Compared to starches, fats are a much more compact reservoir of energy, which is beneficial for animals who move around a lot, unlike plants. Long term food is stored in adipose cells in animals. Fats help protect internal organs. Fats also help insulate the body, as with in whales.

Question 15

What are the smaller molecules that make up a phospholipid?
—- Identify the hydrophilic and hydrophobic portions of the phospholipids. How do these parts explain the production of a “bilayer” when phospholipids are placed in water?

Answer 15

A phospholipid is made up of two fatty acids and one glycerol. A phosphate group with negative electrical charge (also attached to an additional small charged polar molecule) is joined with the glycerol’s third hydroxyl group, making the hydrophilic head of the phospholipid. The rest of the phospholipid, where the hydrocarbon tails are, is mostly hydrophobic. When placed in water, the hydrophilic heads of the molecules are attracted to the water and face outwards, forming the lipid bilayer and shielding the hydrophobic tails from the water.

Question 16

Cholesterol is a very important steroid. Describe the structure and various functions of cholesterol.

Answer 16

Cholesterol is a steroid, so their carbon skeletons have four fused rings. Cholesterol is crucial to the cell membranes of animals, and aids the production of other steroids, like sex hormones.

Question 17

Proteins are VERY, VERY important molecules in the body. They make up 50% of the dry weight of most cells. Describe some of the important functions (5.13) of this diverse class of molecules.

Answer 17

Proteins can accelerate chemical reactions, protect against disease, store amino acids, coordinate an organism’s activities, respond to chemical stimuli, and are responsible for movement and support.

Question 18

What is the relationship between an amino acid, protein and polypeptide?

Answer 18

A polymer of amino acids is a polypeptide, and proteins are molecules made up of one or more polypeptides.

Question 19

List and recognize four major components of an amino acid, and explain how amino acids may be grouped according to the physical and chemical properties of the side chains.

Answer 19

An amino acid has a side chain (R group), amino group, carboxyl group, and an asymmetric carbon atom. Properties of the R group determine the characteristics of the amino acid. Amino acids are grouped according to the properties of their R groups. Nonpolar side chains are hydrophobic, and the other group contains hydrophilic polar side chains. Acidic side chains are generally negative, and basic amino acids are generally positive.

Question 20

Identify a peptide bond and explain how it is formed.

Answer 20

A peptide bond is a covalent bond between two amino acids. When a carboxyl group of one amino acid is adjacent to the amino group of another, a dehydration reaction can result in a peptide bond between the two.

Question 21

Explain what determines protein conformation (structure) and why it is important.
Explain why morphine is able to mimic a naturally occurring endorphin molecule?

Answer 21

The amino acid sequence of each polypeptide that determines what three-dimensional structure the protein will have. This is important because the specific activities of proteins result from the way the proteins are structured. Morphine is able to mimic endorphins because their shapes are both similar, thus having similar functions.

Question 22

Define primary structure.

What bonds are involved in maintaining the primary structure?

Answer 22

The primary structure of a protein is its sequence of amino acids, which are linked by peptide bonds.

Question 23

Define secondary structure
Describe the two types of secondary protein structure.
What bonds are involved in maintaining the secondary structure?

Answer 23

The coils and folds in a polypeptide chain make up the secondary structure of a protein, and are stabilized by hydrogen bonds. One type of secondary structure is the helix, which is a coil held together by hydrogen bonding every fourth amino acid. The second secondary structure type is the pleated sheet, where two or more segments of the polypeptide chain are connected by hydrogen bonds.

Question 24

Define tertiary structure.

What type of molecular interactions and bonds are involved in maintaining the tertiary protein structure?

Answer 24

The tertiary structure is a three-dimensional structure shape stabilized by interactions between the R groups of amino acids. A hydrophobic interaction contributes to tertiary structure. Disulfide bridges are covalent bonds that further reinforce the shape of a protein, and form where two cysteine monomers are brought close together.

Question 25

Using collagen and hemoglobin as examples, describe quaternary protein structure.

Answer 25

Quaternary structure is the overall protein structure that results from aggregating the polypeptide subunits. Collagen is a fibrous protein that has three helical polypeptides intertwined into a larger, stronger triple helix, which helps collagen support connective tissue. Hemoglobin also has quaternary structure, but has four polypeptide subunits.

Question 26

Sickle cell disease is an inherited blood disorder. Explain how a change in a single amino acid causes a change in the primary, secondary, tertiary and quaternary structure. How does this affect the structure and function of the hemoglobin protein?

Answer 26

Sickle cell disease is caused when one amino acid (valine) is substituted for glutamic acid at the position of the sixth amino acid in the primary structure of hemoglobin. Hydrophobic interactions between the sickle cell proteins chain together, which causes clogging in blood vessels.

Question 27

Define denaturation and explain how proteins may be denatured.

Answer 27

Denaturation is when the pH, salt concentration, temperature, or other aspects of the environment are changed, which can destroy the weak chemical bonds and interactions within a protein. Moving a protein from an aqueous environment to a nonpolar solvent can cause it to become denatured.

Question 28

What can happen if a polypeptide does not fold correctly?

Answer 28

When a polypeptide does not fold correctly, it can cause diseases like cystic fibrosis, Alzheimer’s, Parkinson’s, and mad cow disease.

Question 29

Why is it difficult for scientists to determine the structure of intrinsically disordered proteins?

Answer 29

Because a single protein has thousands of atoms, it is difficult for scientists to determine the structure of intrinsically disordered proteins.

Question 30

Describe the characteristics that distinguish nucleic acids from the other major groups of macromolecules.

Answer 30

Nucleic acids are different from the other major groups of macromolecules because they can provide their own directions for replication. Nucleic acids also contain ribose and deoxyribose connected to bases.

Question 31

List the major components of a nucleotide.

Answer 31

The major components of nucleotides are a five-carbon sugar, a nitrogen-containing base, and one to three phosphate groups.

Question 32

There are two families of nitrogenous bases: pyrimidines and purines. For each describe their structure and what bases belong in each family.

Answer 32

A pyrimidine has one six-membered ring of carbon and nitrogen atoms, whose members include cytosine, thymine, and uracil. A purine has a six-membered ring infused to a five-membered ring, and includes adenine and guanine.

Question 33

Describe the three-dimensional structure of DNA.

Answer 33

A DNA molecule has two polynucleotides, held together by hydrogen bonds, that wrap around each other and form a double helix. The two sugar-phosphate backbones run in antiparallel, and are on the outside of the helix. The nitrogenous bases are paired in the interior of the helix.

Question 34

Provide a historical summary of DNA sequencing. What are some of the major advancements of the past 50 years?

Answer 34

The structure of DNA molecules weren’t described until 1953, and then scientists began to understand linear sequences of nucleotide bases and amino acid sequences of proteins. The first chemical techniques for DNA sequencing were developed in the 1970s. Biologists began to sequence the entire human genome in 1990 and completed it in the early 2000s. The Human Genome Project developed more efficient ways for DNA sequencing, and now we can rely on automatic DNA sequencing machines as well as computing power to enable gene sequencing.

Question 35

How can comparing genomic sequences be used as a “tape measure of evolution”?

Answer 35

Species that share a larger proportion of their DNA and protein sequences are more closely related, and also have similar anatomy. DNA carries genetic information inherited by offspring from parents, so it makes sense that gene sequences and protein products of similar species would be shared from one common species.