Amino Acids and Protein Structure

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Questions and Answers

What determines the tertiary structure of a polypeptide chain?

The sequence of amino acids

The pH of the solution

The temperature of the environment

The primary structure of the polypeptide chain (correct)

Why do glutamate, aspartate, histidine, lysine, or arginine disrupt the helix?

They are non-polar amino acids and form strong bonds.

They are non-polar amino acids and form weak bonds.

They are polar amino acids and form hydrogen bonds.

They are charged amino acids and form ionic bonds or repel each other electrostatically. (correct)

What is a characteristic of globular proteins in aqueous solutions?

They have a linear structure

They have a loose, open structure

They are always soluble in water

Their structure is compact, with a high-density of atoms in the core (correct)

What is the fundamental functional and three-dimensional structural unit of a polypeptide?

Protein domain Signup and view all the answers

What type of amino acids can interfere with the formation of the alpha helix?

Amino acids with bulky side chains Signup and view all the answers

What is true about the length of polypeptide chains and their domains?

Polypeptide chains with more than 200 amino acids often have multiple domains Signup and view all the answers

What is the location of hydrophobic side chains in globular proteins?

In the interior of the molecule Signup and view all the answers

What is the characteristic structure of the beta conformation?

A zigzag structure Signup and view all the answers

How are beta sheets often visualized in illustrations of protein structure?

As broad arrows Signup and view all the answers

Why do hydrophilic groups in the interior of globular proteins form hydrogen bonds or electrostatic interactions?

To eliminate the possibility of water molecules binding to these groups Signup and view all the answers

What is the core of a protein domain built from?

Combinations of super-secondary structural elements Signup and view all the answers

What is true about the folding of a peptide chain within a domain?

It occurs independently of folding in other domains Signup and view all the answers

What role do α-helix and β-sheet structures play in globular proteins?

They provide maximal hydrogen bonding for peptide bond components Signup and view all the answers

What is a key difference between alpha helices and beta sheets?

Beta sheets are composed of two or more peptide chains. Signup and view all the answers

What determines the unique three-dimensional structure of each polypeptide?

The sequence of amino acids Signup and view all the answers

What is the result of maximal hydrogen bonding in globular proteins?

The possibility of water molecules binding to hydrophilic groups is eliminated Signup and view all the answers

In what ways can beta strands be arranged in a beta sheet?

Antiparallel or parallel Signup and view all the answers

What are beta turns/loops typically found in?

Globular proteins Signup and view all the answers

What types of interactions cooperate in stabilizing the tertiary structures of globular proteins?

Different types of interactions, including covalent disulfide bonds, hydrophobic interactions, hydrogen bonds, and ionic interactions Signup and view all the answers

What is the function of beta turns/loops in proteins?

To connect successive runs of alpha helix or beta conformation Signup and view all the answers

What is the main characteristic of fibrous proteins?

Highly elongated protein molecules with a single type of secondary structure Signup and view all the answers

Which type of fibrous protein is characterized by being soft and flexible?

β Sheet Signup and view all the answers

What is the principal component of hair, nails, and wool?

Keratin Signup and view all the answers

What is the structure of the α-keratin chain?

A left-handed helix Signup and view all the answers

What is the repeating pattern in each α-keratin chain?

7-residue repeat Signup and view all the answers

What is the characteristic of collagen molecules?

They are composed of three polypeptide chains Signup and view all the answers

What is the amino acid composition of collagen?

30% Gly and 15-30% Pro or Hyp Signup and view all the answers

What is a consequence of abnormal collagen synthesis or structure?

Dysfunction of cardiovascular organs Signup and view all the answers

What is the consequence of the accumulation of spontaneously aggregating proteins in neurodegenerative disorders?

Alzheimer disease Signup and view all the answers

What is the role of the prion protein (PrP) in transmissible spongiform encephalopathies (TSEs)?

Causative agent of TSEs Signup and view all the answers

What is the consequence of misfolding of transthyretin protein?

Irreversible tissue damage Signup and view all the answers

What is the function of transthyretin protein?

Carrying vitamin A and thyroxine Signup and view all the answers

What is the consequence of mutation in the gene coding for transthyretin?

Structural changes leading to misfolding Signup and view all the answers

What percentage of African Americans are carriers of the Val42Ile variant?

3-4% Signup and view all the answers

What is the prevalence of Transthyretin Amyloidosis cardiomyopathy (ATTR-CM) in patients with heart failure?

14% Signup and view all the answers

What is the characteristic of wild-type ATTR?

Present in 25% of patients over 80 years Signup and view all the answers

Study Notes

Protein Structure

The helix structure of a protein can be disrupted by certain amino acids, such as glutamate, aspartate, histidine, lysine, or arginine, which are charged and can form ionic bonds or repel each other electrostatically.
Tryptophan, with its bulky side chains, or valine or isoleucine, which branch at the β-carbon, can also interfere with the formation of an α-helix if they are present in large numbers.

β-Sheet

In the β conformation, the backbone of the polypeptide chain is extended into a zigzag rather than a helical structure.
The zigzag polypeptide chains can be arranged side by side to form a structure resembling a series of pleats.
Hydrogen bonds are formed between adjacent segments of the polypeptide chain.
β-strands are often visualized as broad arrows in illustrations of protein structure.
β-sheets are composed of two or more peptide chains (β-strands), or segments of polypeptide chains, which are almost fully extended.
In β-sheets, the hydrogen bonds are perpendicular to the polypeptide backbone.

β-Bend/Turns

β-bends/turns are normally present in globular proteins.
Nearly 2/3 of the proteins in turns or loops are connecting elements that link successive runs of α-helix or β-conformation.
β-turns connect the ends of two adjacent segments of an antiparallel β-sheet.

Fibrous Proteins

Fibrous proteins are highly elongated protein molecules whose shapes are dominated by a single type of secondary structure.
Examples of fibrous proteins include:
- Coiled coil: Keratin (durable, insoluble, unreactive)
- β sheet: Silk, fibroin of spider web (soft, flexible)
- Triple helix: Collagen (strong, high tensile strength)

Keratin

Keratin is the principal component of hair, nails, wool, horns, hooves, scales, feathers, and shells.
α-keratin is found in mammals, while β-keratin is found in birds and reptiles.
The α-keratin chain is an α-helix, and pairs of α-keratin chains are inter-wound to form a two-chain coiled coil.
Each α-keratin chain consists of ~310 residues having a 7-residue repeat, with residues a and d being nonpolar.

Collagen

Collagen is a triple helix protein that contains three polypeptide chains.
Each chain is a left-handed helix (3 residues/turn), and the three helical chains are twisted together in a right-handed manner to form a superhelical structure.
Collagen has a distinctive amino acid composition, with 30% glycine and 15-30% proline or hydroxyproline.

Collagen Disorders

Abnormal collagen synthesis or structure can cause diseases such as:
- Cardiovascular disorders (aortic and arterial aneurysms and heart valve malfunction)
- Bone disorders (fragility and easy fracturing)
- Skin disorders (poor healing and unusual distensibility)
- Joint disorders (hypermobility and arthritis)
- Eye disorders (dislocation of the lens)
Examples of collagen disorders include:
- Scurvy (vitamin C deficiency)

Tertiary Structure of Globular Proteins

The primary structure of a polypeptide chain determines its tertiary structure.
Globular proteins have a compact, high-density structure with a high degree of close packing.
Hydrophobic side chains are buried in the interior, while hydrophilic groups are generally found on the surface of the molecule.
Hydrophilic groups in the interior of the polypeptide are involved in hydrogen bonds or electrostatic interactions.

Protein Domains

Protein domains are the fundamental functional and three-dimensional structural units of a polypeptide.
Domains are modular units that are built from combinations of super-secondary structural elements (motifs).
Folding of the peptide chain within a domain usually occurs independently of folding in other domains.
Each domain has the characteristics of a small, compact globular protein that is structurally independent of the other domains in the polypeptide chain.

Interactions Stabilizing Tertiary Structure

The unique three-dimensional structure of each polypeptide is determined by its amino acid sequence.
Interactions between the amino acid side chains guide the folding of the polypeptide to form a compact structure.
Different types of interactions cooperate in stabilizing the tertiary structures of globular proteins, including:
- Covalent disulfide bonds
- Hydrophobic interactions
- Hydrogen bonds
- Ionic interactions

Protein Misfolding

Deposits of misfolded proteins are associated with a number of diseases, including amyloidoses.
The prion protein (PrP) has been implicated as the causative agent of transmissible spongiform encephalopathies (TSEs), including Creutzfeldt-Jakob disease in humans, scrapie in sheep, and bovine spongiform encephalopathy in cattle.

Transthyretin Amyloidosis (ATTR)

ATTR occurs as a result of misfolding of the transthyretin protein produced by the liver.
The misfolded protein produces amyloid fibrils that can deposit in various tissues, causing irreversible damage.
Mutation in the gene coding for TTR can cause structural changes leading to misfolding (hATTR); normal aging process can render ATTR tetramer prone to misfolding (wATTR).
ATTR cardiomyopathy (ATTR-CM) is a systemic amyloidosis caused by the accumulation of transthyretin fibrils in the myocardium.

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Description

This quiz covers the effects of different amino acids on protein structure, including those that disrupt the alpha-helix and those that interfere with beta-sheet formation.