Chapter 18 : Protein structure and function

Carbon monoxide binds tightly to the heme groups of hemoglobin and myoglobin. How does this affinity reflect the toxicity of carbon monoxide?

Because carbon monoxide binds tightly to the heme groups of hemoglobin, it is not easily removed or replaced by oxygen. As a result, the effects of oxygen deprivation (suffocation) occur

Describe the forces that maintain the two types of secondary structure: a-helix and b-pleated sheet.

Both the a-helical and b-pleated sheet secondary structures are maintained by hydrogen bonds between the amine hydrogen and the carbonyl oxygen atoms of the peptide bond

Write an equation representing the action of the proteolytic enzyme chymotrypsin. (Hint: In order to write the structure of a dipeptide that would be an appropriate reactant, you must consider what is known about where chymotrypsin cleaves a protein chain.)

Chymotrypsin catalyzes the hydrolysis of peptide bonds on the carbonyl side of aromatic amino acids

Define the term denaturation.

Denaturation is the process by which the organized structure of a protein is disrupted, resulting in a completely disorganized, nonfunctional form of the protein

What is the difference between denaturation and coagulation?

Denaturation occurs when the organized secondary, tertiary, and quaternary structures of a protein become completely disorganized. Loss of the correct three-dimensional shape results in loss of function. Coagulation occurs when protein molecules clump together. Proteins do not need to be denatured in order to coagulate.

Explain why a-keratins that have many disulfide bonds between adjacent polypeptide chains are much less elastic and much harder than those without disulfide bonds

Disulfide bonds are covalent crosslinks between cysteine residues within a protein chain or in different protein chains. Such crosslinks will restrict the independent movement of individual protein chains that are bound together and will restrict the motion (elasticity) within a single peptide chain that has internal disulfide bonds.

How do antibodies protect us against infection?

Each antibody has regions that precisely fit and bind to a single antigen. They protect us by precisely binding to the foreign antigen. If the antigen is a virus particle, antibody binding directly neutralizes the virus. If the pathogen is a bacterium, antibody binding facilitates its destruction or removal from the body.

Provide two examples of nutrient proteins

Egg albumin is a nutrient protein that serves as a source of protein for the developing chick. Casein is the nutrient storage protein in milk, providing protein, a source of amino acids, for mammals.

Of what significance are enzymes in the cell?

Enzymes speed up reactions that might take days or weeks to occur on their own. They also catalyze reactions that might require very high temperatures or harsh conditions if carried out in the laboratory. In the body, these reactions occur quickly under physiological conditions.

Why is heat an effective means of sterilization?

Heat is an effective means of sterilization because it destroys the proteins of microbial life-forms, including fungi, bacteria, and viruses

Describe the structure of hemoglobin.

Hemoglobin is a protein composed of four subunits—two a-globin and two b-globin subunits. Each subunit holds a heme group, which in turn carries an Fe2 + ion.

Why is hydrogen bonding so important to protein structure?

Hydrogen bonding maintains the secondary structure of a protein and contributes to the stability of the tertiary and quaternary levels of structure

Compare a parallel b-pleated sheet to an antiparallel b-pleated sheet.

In a parallel b-pleated sheet, the hydrogen bonded peptides have their N-termini aligned head-to-head. In an antiparallel b-pleated sheet, the N-terminus of one chain is aligned with the C-terminus of the second chain

What is the importance of the R groups of the amino acids?

Interactions between the R groups of the amino acids in a polypeptide chain are important for the formation and maintenance of the tertiary and quaternary structures of proteins.

Describe the structure of myoglobin.

Myoglobin is a globular protein consisting of a single protein subunit. It has a heme group bearing an Fe2+ ion.

What is the function of myoglobin?

Myoglobin is the oxygen storage protein found in muscle tissue

Draw the d- and l-isomers of valine. Which would you expect to find in nature?

One would expect the L-isomer of valine to be found in nature

What type of bond joins the amino acids to one another in the primary structure of a protein?

Peptide, or amide, bonds join the amino acids to one another in the primary structure of a protein.

Why is the amino acid proline often found in the random coil hinge regions of the tertiary structure?

Proline is generally found in the random coil hinge region of the tertiary structure because its cyclic structure disrupts an a-helix.

How does the structure of the peptide bond make the structure of proteins relatively rigid

The peptide bond exhibits resonance, which results in a partially double bonded character. This causes the rigidity of the peptide bond.

What type of secondary structure is characteristic of: a. The a-keratins? b. Silk fibroin?

a. a-Helix b-Pleated sheet

What is the most abundant protein in the blood?

albumin

What is a chiral carbon?

A chiral carbon is one that has four different atoms or groups of atoms attached to it

Why is oxygen efficiently transferred from hemoglobin in the blood to myoglobin in the muscles?

Oxygen is efficiently transferred from hemoglobin to myoglobin in the muscle because myoglobin has a greater affinity for oxygen.

Describe the quaternary structure of proteins

Quaternary protein structure is the aggregation of two or more folded peptide chains to produce a functional protein

What is the function of regulatory proteins?

Regulatory proteins control many aspects of cellular function, including metabolism, gene expression, and reproduction.

Write the structures of the six amino acids that have polar, neutral side chains.

Serine, threonine, tyrosine, cysteine, asparagine, glutamine

Why are amino acids zwitterions at pH 7.0

Amino acids are zwitterions at pH7 because the carboxyl group is in the conjugate base form (-COO-) and the amino group is in the conjugate acid form (-N+H3).

Define fibrous proteins

A fibrous protein is one that is composed of peptides arranged in long sheets or fibers.

What is a glycoprotein?

A glycoprotein is a protein with covalently attached sugars.

Define the term nonessential amino acid.

A nonessential amino acid is one that can be synthesized by the body.

Describe a parallel b-pleated sheet.

A parallel b-pleated sheet is one in which the hydrogen bonded peptide chains have their amino-termini aligned head-to-head.

Define the term peptide bond.

A peptide bond is an amide bond between two amino acids in a peptide chain.

Provide two examples of proteins that are required for movement.

Actin and myosin are two proteins in muscle that are required for movement. The flagella responsible for motility in bacteria are composed of the protein flagellin.

Why are all of the a-amino acids except glycine chiral?

All amino acids except glycine are chiral because the a-carbon of each is bonded to four different chemical groups.

Define the term antibody.

An antibody is a specific glycoprotein (protein with attached carbohydrate groups) produced by cells of the immune system in response to invasion by an infectious agent.

Define the term enzyme

An enzyme is a protein that serves as a biological catalyst, speeding up biological reactions.

Define the term essential amino acid.

An essential amino acid is one that must be provided in the diet because it cannot be synthesized in the bod

Define the term incomplete protein.

An incomplete protein is one that does not contain all of the essential and nonessential amino acids.

What is the role of cystine in maintaining protein structure?

Cystine is produced in the oxidation reaction between two cysteine molecules located in different locations along the peptide chain. The disulfide bridge of cystine holds these distant regions of the peptide chain together in the folded tertiary structure of the protein.

What observations led Linus Pauling and his colleagues to hypothesize that the peptide bond exists as a resonance hybrid?

Linus Pauling and his colleagues carried out X-ray diffraction studies of protein. Interpretation of the pattern formed when X-rays were diffracted by a crystal of pure protein led Pauling to conclude that peptide bonds are both planar (flat) and rigid and that the N—C bonds are shorter than expected. In other words, they deduced that the peptide bond has a partial double bond character because it exhibits resonance. There is no free rotation about the amide bond because the carbonyl group of the amide bond has a strong attraction for the amide nitrogen lone pair of electrons.

What are the functions of structural proteins?

Structural proteins provide structural support for animals and plants. They include proteins such as the collagens and keratins.

What does it mean to say that the structure of proteins is genetically determined?

The code for the primary structure of a protein is carried in the genetic information (DNA).

What is the relationship between the structure of fibrous proteins and their functions?

The coiled-coil and sheet-like structures of fibrous proteins have great mechanical strength. Thus they are good components of muscle, skin, hooves, nails, and hair.

Wine is made from the juice of grapes by varieties of yeast. The yeast cells produce ethanol as a by-product of their fermentation. However, when the ethanol concentration reaches 12-13%, all the yeast die. Explain this observation.

The ethanol produced by the yeast will denature yeast proteins and may dissolve yeast membranes.

Explain the relationship between the primary structure of a protein and the gene for that protein.

The genetic information in the DNA dictates the order in which amino acids will be added to the protein chain. The order of the amino acids is the primary structure of the protein. The code for the primary sequence of a protein is carried by the genes.

Yogurt is produced from milk by the action of dairy bacteria. These bacteria produce lactic acid as a by-product of their metabolism. The pH decrease causes the milk proteins to coagulate. Why are food preservatives not required to inhibit the growth of bacteria in yogurt?

The low pH of the yogurt denatures the proteins of microbial contaminants, inhibiting their growth.

What are the two most common types of secondary structure?

The most common types of secondary structure are the a-helix and the b-pleated sheet.

What type of bond is the peptide bond? Explain why the peptide bond is rigid

The peptide bond is an amide bond. Although you might expect there to be free rotation around the -N-C-C- single bonds of the peptide backbone, this is not the case. The peptide bond has a partially double bond character because it exhibits resonance. As a result, peptide bonds are both planar (flat) and rigid and the N-C bond is shorter than expected.

Write the structures of the positively charged amino acids. Indicate whether you would expect to find each on the surface or buried in a globular protein.

The positively charged amino acids all have polar, hydrophilic R groups. Therefore, they would tend to be on the surface of a protein. Lysine, Arginine, Histidine

The blood of the horseshoe crab is blue because of the presence of a protein called hemocyanin. What is the function of hemocyanin?

The prefix hemo- suggests that this is a heme-containing pigment with a function similar to hemoglobin, i.e., it is carrying oxygen in the blood of the horseshoe crab.

The primary structure of a protein known as histone H4, which tightly binds DNA, is identical in all mammals and differs by only one amino acid between the calf and pea seedlings. What does this extraordinary conservation of primary structure imply about the importance of that one amino acid?

The primary amino acid sequence of a protein determines the secondary and tertiary structure that the protein will eventually assume. Since the primary structures of histones from such diverse sources are so similar, the three-dimensional conformation of the protein must be critical to its function. Changes in the primary structure that alter the three-dimensional conformation render the histone protein nonfunctional. Thus, the amino acid sequence has remained remarkably constant over evolutionary time. The single amino acid that is altered in the pea must have little impact on the overall three-dimensional folding of histone H4.

How is oxygen efficiently transferred from mother to fetus?

Fetal hemoglobin has a greater affinity for oxygen than adult hemoglobin. As a result, oxygen is efficiently transferred from maternal to fetal blood.

Define the primary structure of a protein

The primary structure of a protein is the sequence of amino acids bonded to one another by peptide bonds.

Define the secondary structure of a protein

The secondary structure of a protein is the folding of the primary structure into an a-helix or b-pleated sheet.

Why must synthesis of digestive enzymes be carefully controlled?

Synthesis of digestive enzymes must be carefully controlled because the active enzyme would digest, and thus destroy, the cell that produces it

What are some common sources of dietary protein?

Common sources of dietary protein include fish, meats, dairy products, and a variety of beans.

How does high temperature denature proteins?

High temperature disrupts the hydrogen bonds and other weak interactions that maintain protein structure

Why is it necessary to mix vegetable proteins to provide an adequate vegetarian diet?

In a vegetarian diet, vegetables are the only source of dietary protein. Because most individual vegetable sources do not provide all the needed amino acids, vegetables must be mixed to provide all the essential and nonessential amino acids in the amounts required for biosynthesis.

As you increase the temperature of an enzyme-catalyzed reaction, the rate of the reaction initially increases. It then reaches a maximum rate and finally dramatically declines. Keeping in mind that enzymes are proteins, how do you explain these changes in reaction rate?

Initially the increase in temperature increases the frequency of the collisions between substrate and enzyme. This causes an increase in the reaction rate. As long as the temperature is below that which causes denaturation of protein structure, the reaction rate will continue to increase with increases in temperature. However, at a certain temperature, which is characteristic for each particular enzyme, the additional heat energy will begin to interfere with the weak interactions that maintain the essential three-dimensional structure of the enzyme. When the conformation of the enzyme active site loses its characteristic three-dimensional shape or its characteristic charge distribution, the enzyme is no longer functional.

How does the primary structure of a protein determine its three-dimensional shape and biological function?

The primary structure of a protein determines its three dimensional shape and biological function because the location of R groups along the protein chain is determined by the primary structure. The interactions among the R groups, based on their location in the chain, will govern how the protein folds. This, in turn, dictates its three-dimensional structure and biological function

Describe the four levels of protein structure.

The primary structure of a protein is the amino acid sequence of the protein chain. Regular, repeating folding of the peptide chain caused by hydrogen bonding between the amide nitrogens and carbonyl oxygens of the peptide bond is the secondary structure of a protein. The two most common types of secondary structure are the a-helix and the b-pleated sheet. Tertiary structure is the further folding of the regions of the a-helix and b-pleated sheet into a compact, spherical structure. Formation and maintenance of the tertiary structure results from weak attractions between amino acid R groups. The binding of two or more peptides to produce a functional protein defines the quaternary structure.

Name some ethnic foods that apply the principle of mixing vegetable proteins to provide all of the essential amino acids.

A variety of ethnic foods that apply the principle of mixing vegetable protein sources include Mexican tortilla and beans, Cajun spicy rice and beans, baked beans and cornbread, and Indian bean and lentil dishes.

Define the term complete protein.

A complete protein is one that contains all of the essential and nonessential amino acids.

Explain why genetic mutations that result in the replacement of one amino acid with another can lead to the formation of a protein that cannot carry out its biological function.

A mutation may replace an amino acid of one R group class with an amino acid of another class. For example, a polar amino acid may be replaced by a hydrophobic amino acid. If the original amino acid was involved in hydrogen bonding that was essential to maintain the structure of the protein, the protein will be inactive when that amino acid is replaced by a hydrophobic amino acid that cannot participate in hydrogen bonding.

What is a prosthetic group?

A prosthetic group is a nonprotein group required in order for a protein to function. An example is the heme group of hemoglobin and myoglobin.

What is a transport protein?

A transport protein is a protein that transports materials across the cell membrane or throughout the body

What is a zwitterion?

A zwitterion is a neutral molecule with equal numbers of positive and negative charges. Under physiological conditions, amino acids are zwitterions.

Develop a hypothesis to explain why albumin in the blood can serve as a nonspecific carrier for such diverse substances as bilirubin, Ca21, and fatty acids. (Hint: Consider what you know about the structures of amino acid R groups.)

Albumin in the blood can serve as a carrier for Ca21 because it contains acidic amino acids. The negative charges in the acidic amino acids can form salt bridges (or ionic bonds) with Ca21. Albumin can also serve as a carrier for fatty acids because it contains basic amino acids. The positive charges in the basic amino acids can form salt bridges with the anionic fatty acids.

Describe the classification of the R groups of the amino acids, and provide an example of each class.

Amino acids are classified on the basis of the properties of the R groups. Leucine is an example of a nonpolar, hydrophobic amino acid. Serine is a polar, neutral amino acid. Under physiological conditions, glutamate is a negatively charged amino acid and arginine is a positively charged amino acid.

How does extremely low pH cause proteins to coagulate?

At low pH, the carboxylate groups of a protein become protonated. When the protein becomes electrically neutral, it can no longer interact with water molecules. As a result it cannot remain in solution and the protein molecules clump together and coagulate into a solid curd. Low pH may also disrupt hydrogen bonding and ionic bridges between R groups and disrupt secondary, tertiary, and quaternary structure of the protein.

What is the relationship between pepsin and pepsinogen

Pepsin is the active form of the enzyme that begins digestion of protein in the stomach. It is secreted in an inactive form called pepsinogen. This inactive precursor is activated when a segment is proteolytically cleaved away

What weak interactions are responsible for maintaining quaternary protein structure?

The forces responsible for maintaining quaternary structure are hydrogen bonding, ionic bridges, van der Waals forces, and disulfide bonds.

What is the function of hemoglobin?

The function of hemoglobin is to carry oxygen from the lungs to oxygen-demanding tissues throughout the body. Hemoglobin is found in red blood cells

What is the function of heme in hemoglobin and myoglobin?

The function of the heme group in hemoglobin and myoglobin is to bind to molecular oxygen

Describe the basic general structure of an l-a-amino acid, and draw its structure.

The general structure of an l-a-amino acid has a carbon in the center that is referred to as the alpha carbon. Bonded to the alpha carbon are a protonated amino group, a carboxylate group, a hydrogen atom, and a side chain, R.

How is it possible for sickle cell trait to confer a survival benefit on the person who possesses it?

The sickle cell mutation first appeared in west or central Africa, where malaria is a leading cause of death. Because an individual with one normal b-globin gene and one sickle cell b-globin gene is more resistance to malaria, they tend to live longer and produce more offspring. Thus, the gene became increasingly common in the population.

How do sickled red blood cells hinder circulation?

The sickle cells are elongated. These elongated cells become stuck in the small capillaries, thereby blocking blood flow.

Explain the relationship between the secondary and tertiary protein structures.

The tertiary structure is a level of folding of a protein chain that has already undergone secondary folding. The regions of a-helix and b-pleated sheet are folded into a globular structure.

Define the tertiary structure of a protein

The tertiary structure of a protein is the globular, three dimensional structure of a protein that results from folding the regions of secondary structure.

What are the weak interactions that maintain the tertiary structure of a protein?

The weak attractions that maintain the tertiary structure of a protein are interactions between amino acid R groups. These include the following:a. hydrogen bonding between polar amino acid R groups b. ionic bridges between positively and negatively charged amino acid R groups c. van der Waals attractions between nonpolar amino acid R groups d. covalent bonding (disulfide bonds) between two cysteines

List the functions of several a-globulins.

There are many different types of α-globulins. Both very low-density lipoproteins and high-density lipoproteins are examples of α-globulins that are responsible for the transport of lipids in the body. Haptoglobin is a transport protein for free hemoglobin. Ceruloplasmin is a copper transport protein. Prothrombin is involved in blood clotting. The most abundant α-globulin is α1-antitrypsin, a protein that inactivates an enzyme that causes damage in the lungs.

List two transport proteins and describe their significance to the organism.

Transferrin is a transport protein that carries iron from the liver to the bone marrow, where it is used to produce the heme group for hemoglobin and myoglobin. Hemoglobin transports oxygen in the blood.

Use examples of specific amino acids to show the variety of weak interactions that maintain tertiary protein structure.

Two polar amino acids, such as serine and threonine, can hydrogen bond to one another via their hydroxyl groups. The hydrophobic amino acids phenylalanine and tryptophan would associate through van der Waals attractions. The positively charged amino acid arginine could form an ionic bridge with the negatively charged amino acid glutamate. Two cysteines can covalently bond to form a disulfide bridge.

Why must vegetable sources of protein be mixed to provide an adequate diet?

Vegetables vary in amino acid composition. Most vegetables do not provide all of the amino acid requirements of the body. By eating a variety of different vegetables, all the amino acid requirements of the human body can be met.

Fibrinogen and prothrombin are both involved in formation of blood clots when they are converted into proteolytic enzymes. However, they are normally found in the blood in an inactive form. Develop an explanation for this observation.

When fibrinogen and prothrombin are found in the blood, they are in their inactive forms because they are proteolytic enzymes. The active enzymes would hydrolyze the peptide bonds of the blood proteins which would destroy the proteins in the blood

What is the difference between sickle cell disease and sickle cell trait?

When individuals have one copy of the sickle cell gene and one copy of the normal gene, they are said to carry the sickle cell trait. These individuals will not suffer serious side effects,but may pass the trait to their offspring. Individuals with two copies of the sickle cell globin gene exhibit all the symptoms of the disease and are said to have sickle cell anemia.

Why does replacement of glutamic acid with valine alter hemoglobin and ultimately result in sickle cell anemia?

When sickle cell hemoglobin (HbS) is deoxygenated, the amino acid valine fits into a hydrophobic pocket on the surface of another HbS molecule. Many such sickle cell hemoglobin molecules polymerize into long rods that cause the red blood cell to sickle. In normal hemoglobin, glutamic acid is found in the place of the valine. This negatively charged amino acid will not "fit" into the hydrophobic pocket.