CHAPTER 9 or 19

Proteins

 Section 1   Section 2  Section 3   Section 4

Section 5  Section 6   Section 7   Section 8

Section 9  Section 10

 

 

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SECTION 9.1  The Amino Acids

 

1.  Proteins are polymers of amino acids.

 

The building blocks of proteins are ________.

 

2.  There are 20 common amino acids found in proteins.

 

How many amino acids are commonly present in proteins?

 

3.  The amino acids in proteins (see Figure 9.1) are called alpha (a)-amino acids because an amino group is attached to the alpha carbon, the one next to the carboxylate group.

 

In amino acids, the carbon next to the carboxylate group is called the ________ carbon.

 

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SECTION 9.2  Zwitterions

 

4.  Amino acids transfer a hydrogen ion in a kind of internal acid-base reaction to form a dipolar ion called a zwitterion (see Reaction 9.1).

 

Amino acids exist as dipolar ions called ________.

 

5.  In the general formula for an alpha amino acid in zwitterionic form, the carboxylate group (-COO-) has a negative charge and the amino group (-NH3+) has a positive charge:

 

In a zwitterion form of an amino acid, which group is negatively charged?

 

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SECTION 9.3  Reactions of Amino Acids

 

6.  Cysteine, an amino acid with an –SH containing side chain, undergoes oxidation (see  Reaction 9.4) to produce a disulfide bond (-S-S-).

 

When an amino acid containing an –SH group is oxidized, what group is formed in the product?

 

7.  When a carboxylate group of one amino acid reacts with the amino group of a second amino acid, an amide group is formed (see Reaction 9.5).  In protein chemistry, the amide linkage is called a peptide linkage or peptide bond.

 

a) When two amino acids react to form an amide group, the linkage may be referred to as a ________ linkage.

b)  Draw the peptide linkage that will form when 2 alanine molecules react.  Label the amide linkage.

8.  Compounds made up of two amino acids linked together are called dipeptides (see Reaction 9.6).

 

A dipeptide consists of ________ amino acids joined together by a peptide linkage.

 

9.  When several amino acids are linked together, the compounds are often simply called peptides.

 

Peptides consist of chains of ________.

 

10.  Compounds with chains of amino acids are called polypeptides.

 

Polypeptides consist of long chains of _______.

 

11.  When polypeptide chains contain more than 50 amino acids, the compounds are called proteins.  However, the terms polypeptide and protein are often used interchangeably.

 

A polypeptide chain with more than 50 amino acids is generally called a ________.

 

12.  Amino acids that have been incorporated into chains are called amino acid residues.

 

The amino acids within a peptide are called amino acid ________.

 

13.  The amino acid residue with an unreacted or free amino group is called the N-terminal residue.

 

The N-terminal residue is the amino acid with an unreacted ________ group.

 

14.  By convention, the N-terminal residue is placed on the left in a peptide or protein structure.

 

On which end of a peptide structure is the N-terminal residue located?

 

15.  The residue with a free carboxylate group is called the C-terminal residue.

 

The residue in a peptide which has an unreacted carboxylate group is called a ________ terminal residue.

 

16.  By convention, the C-terminal residue is placed on the right in a peptide or protein structure.

 

a)  On which end of a peptide structure is the C-terminal residue located?

b)  Cys-Leu-Val-Ala

Answer the following questions about the peptide above.

1)  What amino acid is the C-terminal end?

2)  What amino acid is the N-terminal end?

3)  What amino acid has an unreacted carboxylate group?

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SECTION 9.4   Important Peptides

 

17.  More than 200 peptides have been identified as essential to proper functioning of the human body (see Table 9.2).  Two important peptides, vasopressin and oxytocin, each contain a disulfide bond which draws the peptide chain into a loop.  Such disulfide bonds are called disulfide bridges (see Figure 9.2).

 

The presence of a disulfide bond in a protein structure is referred to as a disulfide ________.

 

18.  Vasopressin is known as antidiuretic hormone (ADH) because of its action in reducing the volume of urine formed, thus conserving the body’s water.

 

Another name for ADH, antidiuretic hormone, is ________.

 

19.  Oxytocin causes the smooth muscles of the uterus to contract and is often administered to induce labor.

 

What peptide is often used to induce labor?

 

20.  Another important peptide hormone is adrenocorticotropic hormone (ACTH), which regulates the production of steroid hormones in the cortex of the adrenal gland.

 

The letters ACTH represent the important peptide adrenocorticotropic ________.

 

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SECTION 9.5  Characteristics of Proteins

 

21.  Proteins serve in a wide variety of important ways.  One way of classifying proteins is by function (see Table 9.4).  A large number of proteins have a catalytic function.  Nearly all the reactions that take place in living organisms are catalyzed by proteins functioning as enzymes.

 

Proteins serving a catalytic function are called ________.

 

22.  An example of a protein with a structural function is keratin, the chief constituent of hair, skin, and fingernails.  Another structural protein is collagen, which is found in connective tissue.

 

The protein of skin is called ________.

 

23.  Some proteins provide a way to store small molecules or ions.  Ferritin, a liver protein, attaches to iron ions and forms a storage complex.

 

A protein with a storage function, ferritin, acts to store ________ ions.

 

24.  Antibodies are tremendously important proteins with a protective function.  They protect from disease caused by the invasion of foreign materials.

 

An example of proteins which serve a protective function are the ________.

 

25.  Numerous body processes are regulated by proteins.  Insulin, a protein with a regulatory function, helps to control glucose metabolism.

 

A regulatory protein involved in controlling glucose metabolism is ________.

 

26.  Some proteins are important in nerve impulse transmission.  Rhodopsin, a protein found in the rod cells of the retina of the eye, helps nerve impulse transmission in the vision process.

 

A protein important in the vision process is ________.

 

27.  The proteins actin and myosin are important in muscle movement.  They are long-filament proteins that slide along each other during muscle contraction.

 

Two proteins associated with movement function are actin and ________.

 

28.  Numerous small molecules and ions are transported through the body by binding to proteins.  The blood protein hemoglobin serves a transport function by carrying oxygen from the lungs to other body tissues. 

 

A protein which transports oxygen within the bloodstream is ________

 

29.  A second classification scheme for proteins is based on their structural shape.  Proteins are either fibrous or globular in shape.  Fibrous proteins are made up of string-like molecules that can intertwine and form strong fibers.

 

Proteins which form fibers are classified as ________ proteins.

 

30.  Fibrous proteins are water-insoluble and are found as components of connective tissue (collagen) and hair and skin (keratin).

 

An example of a fibrous protein is ________, found in connective tissue.

 

31.  Globular proteins are more spherical and more soluble in water than fibrous proteins.

 

Proteins with a spherical shape are called ________ proteins.

 

32.  Examples of globular proteins are the transport proteins (hemoglobin) and the catalytic proteins (enzymes).

 

Are enzymes more likely fibrous or globular proteins?

 

33.  A third method of classifying proteins is based on composition; proteins are either simple or conjugated.  Simple proteins are those that contain only amino acid residues.

 

Proteins which contain only amino acid residues are called ________ proteins.

 

34.  Conjugated proteins contain amino acid residues and other organic or inorganic components (see Table 9.5).

 

Would hemoglobin, an iron-containing protein, be classified as simple or conjugated?

 

35.  The non-amino acid parts of conjugated proteins are called prosthetic groups.

 

Are prosthetic groups a part of the structure of simple or conjugated proteins?

 

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SECTION 9.6  The Primary Structure of Proteins

 

36.  The order in which amino acid residues are linked together in a protein is called the primary structure.

 

The primary structure of a protein refers to the sequence of ________ residues.

 

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SECTION 9.7  The Secondary Structure of Proteins

 

37.  There are two types of secondary protein structure:  α-helix (alpha-helix) and the β-pleated (beta-pleated) sheet.

 

Two types of secondary structure are the β-pleated sheet and the ________.

 

38.  Both types of secondary structure are held together by hydrogen bonds between carbonyl oxygens and amide hydrogens of the peptide bonds (see Figure 9.6).

 

What bonding forces hold the α-helix in its coil-like shape?

 

39.  The α-helix is a helical structure while the β-pleated sheet has protein chains aligned side-by-side in a sheet-like array (see Figure 9.8).

 

Which secondary structure has protein chains aligned side-by-side?

 

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SECTION 9.8  The Tertiary Structure of Proteins

 

40.  The tertiary structure of proteins refers to the bending and folding of the protein into a specific three-dimensional shape held together by interactions between side chains (R-groups).

 

What protein structure results from the interaction of side chains?

 

41.  There are four types of R-group interactions (see Figure 9.10): disulfide bridges (-S-S-), salt bridges (between positive –NH3+ groups and negative carboxylate groups, -COO-), hydrogen bonds, and hydrophobic interactions between nonpolar groups.

 

a)  What type of protein structure is involved when disulfide bridges form?

Hydrogen bonding between peptide linkages gives rise to secondary structure, whereas hydrogen bonding between ________ gives rise to tertiary structure.

The interaction of positive and negative R-groups to give rise to tertiary structure is referred to as ________ bridges.

What types of groups are involved in hydrophobic interactions?

b)  Refer to Table 9.1 in your text and list the type of side-chain interaction expected between the side chains of the following amino acid residues:

1) tyrosine and glutamine

2) aspartate and lysine

3) leucine and isoleucine

4)  phenylalanine and valine

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 Self Test Questions:

1.  Identify what type of side chain interactions each of the following amino acid side chains could form in the tertiary structure of a protein.  The amino acid backbone is attached to the left hand (blank bond) side of the side chain.

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SECTION 9.9  The Quaternary Structure of Proteins

 

42.  Many proteins contain two or more polypeptide chains, called subunits, held together by bonding forces.

 

When a protein is comprised of two or more chains, these individual chains are referred to as ________.

 

43.  The arrangement of subunits to form a larger protein is called the quaternary structure of the protein.

 

The protein structure that results from a collection of subunits is called ________.

 

44.  Hemoglobin is a well-known example of a protein exhibiting quaternary structure.  It has four chains.

 

Name a protein that exhibits quaternary structure.

 

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SECTION 9.10  Protein Hydrolysis and Denaturation

 

45.  When proteins are completely hydrolyzed by acid, base or enzymes, the products are amino acids (see Reaction 9.9).  All levels of protein structure are destroyed.

 

The products of complete protein hydrolysis are ________.

 

46.  The natural three-dimensional structure of proteins is called the native state.

 

The natural conformation of a functioning protein is called the ________ state.

 

47.  When proteins are exposed to conditions which break down the native state and the protein takes on a random, disorganized conformation, the process is called denaturation (see Figure 9.13).

 

When a protein loses its specific three-dimensional structure, the process is called ________.

 

48.  Denaturation involves the loss of secondary, tertiary and quaternary structure.  But, the protein chain (primary structure) remains intact.

 

a)  Which level of protein structure is not destroyed during denaturation?

b)  Which level of protein structure is not destroyed during protein hydrolysis?

 

49.  Denaturation causes the protein to become inactive and it may precipitate.  The precipitation of egg protein during cooking is an example of protein denaturation.

 

Protein denaturation is accompanied by a loss of function and the protein may ________ from solution.

Heating may cause protein ________.

 

50.  Heavy metal ions such as Hg2+, Ag+ and Pb2+ can cause the denaturation of proteins.  Mercury, silver and lead salts are toxic because of this.

 

Heavy metal ions such as those of mercury, silver and ________ can cause protein denaturation.

 

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