Secondary Structure in Proteins

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Questions and Answers

What is the time scale in which conformational changes in proteins typically occur?

10^1 to 10^4 s

10^-6 to 10^-3 s

10^-12 to 10^-6 s

10^-9 to 10^3 s (correct)

What structural feature is primarily stabilized by right-handed twists in proteins?

Primary structure

Tertiary structure (correct)

Secondary structure

Quaternary structure

Which types of connections join adjacent antiparallel β-strands?

Helices

Loops

Hairpins (correct)

Crossovers

How does proline cis-trans isomerization affect protein structure?

It can switch on/off protein activity. Signup and view all the answers

What is the expected distance that conformational changes can cover?

As large as 1 nm Signup and view all the answers

Which component is typically found between layers of α-helix in certain protein domains?

β-sheet Signup and view all the answers

What kind of molecular interactions are involved in the conformational changes of proteins?

Specific interactions within the protein Signup and view all the answers

Which characteristic of polypeptide chains contributes to the formation of variety in tertiary structures?

Right-handed twists Signup and view all the answers

What is the effect of hydrophobic side chains in a protein structure?

They tend to cluster together to minimize exposure to water. Signup and view all the answers

Which type of proteins typically play a structural role in nature?

Fibrous proteins Signup and view all the answers

How do fibrous proteins mainly organize their structure?

In approximately parallel polypeptide chains along a single axis. Signup and view all the answers

What structural feature is dominant in α-keratins?

α-helical segments of polypeptides. Signup and view all the answers

What potential problem arises in the simplicity of the folding model for proteins?

Polar backbone groups contribute to energetically costly interiors. Signup and view all the answers

What is the role of terminal cap domains in α-keratin molecules?

They stabilize interactions between central rod domains. Signup and view all the answers

Which feature characterizes keratin filaments in terms of their structural composition?

Bundled coiled coils forming protofilaments. Signup and view all the answers

Why are hydrophobic side chains energetically costly in protein folding?

They disrupt the hydrogen bonding structure of water when inside the protein. Signup and view all the answers

What effect does a decreased surface-to-volume ratio have on proteins?

It usually results in more stable proteins. Signup and view all the answers

What is the primary function of molecular chaperones?

To aid in the correct folding of proteins Signup and view all the answers

Why is oligomeric association considered genetically economical?

Less DNA is needed to code for a monomer that forms a homomultimer. Signup and view all the answers

Which of the following statements about TIM barrels is true?

Triose phosphate isomerase is an example of a TIM barrel protein. Signup and view all the answers

In the context of enzymes, what role does oligomeric association play?

It brings necessary catalytic groups together to form active enzymes. Signup and view all the answers

How do most oligomeric enzymes regulate their catalytic activity?

Through cooperative phenomena and subunit interactions. Signup and view all the answers

Why might proteins with similar structures not share similar functions?

Functional diversity can arise from different sequences. Signup and view all the answers

How many structures does the Protein Data Bank currently curate?

Over 200,000 Signup and view all the answers

What characterizes positive cooperativity in multisubunit proteins?

Increased affinity at subsequent binding sites. Signup and view all the answers

What is the outcome of negative cooperativity in proteins?

It decreases the affinity at subsequent binding sites. Signup and view all the answers

What is the role of heat shock proteins such as Hsp70?

They protect cells from temperature-induced stress. Signup and view all the answers

What does the term 'allostery' refer to in the context of protein function?

Changes in protein structure affecting function at distant sites. Signup and view all the answers

What is a significant characteristic of bacterial glutamine synthetase's active sites?

The active sites are completed by pairs of adjacent subunits. Signup and view all the answers

What characterizes the stability of secondary structures like α-helices and β-pleated sheets?

Hydrogen bonds between peptide groups Signup and view all the answers

How many amino acid residues are typically found in one turn of an α-helix?

3.6 residues Signup and view all the answers

What direction do all hydrogen bonds in an α-helix point?

Parallel to the helix axis Signup and view all the answers

What is the typical average length of an α-helix in terms of number of residues?

10 residues Signup and view all the answers

In a paralel β-pleated sheet, how do adjacent peptide chains align?

They run in the same direction Signup and view all the answers

What is the characteristic distance between residues in a typical antiparallel β-pleated sheet?

0.347 nm Signup and view all the answers

Which of the following statements accurately describes the arrangement of hydrogen bonds in a β-pleated sheet?

H bonds form between adjacent strands Signup and view all the answers

What type of structure provides both flexibility and strength in spider silk?

Helix-sheet composite structures Signup and view all the answers

How do nonpolar residues located near the termini of an α-helix typically behave?

They can be exposed to the solvent Signup and view all the answers

What is a defining feature of parallel β-pleated sheets compared to antiparallel ones?

More regular and consistent structure Signup and view all the answers

What effect does the shearing force have on keratin protein during silk extrusion from a spider's glands?

It breaks hydrogen bonds stabilizing α-helices Signup and view all the answers

What is the pitch of an α-helix, given it is made of 3.6 residues per turn?

5.4 Å Signup and view all the answers

Which of the following statements correctly describes the H bonding pattern in an α-helix?

Each carbonyl bonds to the N-H of the residue four positions earlier Signup and view all the answers

Study Notes

Secondary Structure of Proteins

Secondary structure refers to local conformations of polypeptides stabilized by hydrogen bonds.
Hydrogen bonds form between the amide proton of one peptide group and the carbonyl oxygen of another.
Common secondary structures include α-helices and β-pleated sheets.

α-Helix Structure

One turn of the helix consists of 3.6 amino acid residues.
Each amino acid residue contributes 1.5 Å (0.15 nm) along the helix axis with a total pitch of 5.4 Å (0.54 nm).
Average length of an α-helix is typically 10 residues, but this can vary.
Each carbonyl in the helix forms an H bond with the N-H group of a residue located four residues upstream.
H bonds are oriented parallel to the helix axis, creating a significant dipole moment.
Charged ligands (e.g., phosphates) often bind to the positively charged N-terminus of the α-helix.

β-Pleated Sheet Structure

Visualized as pleated strips or zigzag patterns formed by peptide strands.
Parallel β-sheets have adjacent chains running in the same direction with a spacing of 0.325 nm.
Antiparallel β-sheets consist of chains running in opposite directions with a distance of 0.347 nm.
β-sheets require an alternating arrangement of hydrophilic and hydrophobic residues.
Side chains extend out perpendicularly from the pleated sheet structure.

Spider Silk Composition

Spider silk is a keratin with exceptional tensile strength, 200,000 psi, surpassing steel.
Silk's strength and flexibility arise from its composite structure of keratin.
Keratin is extruded from spider glands, initially holding H bonds in α-helices, which transform into β-sheet microcrystals upon stress.
The unique structure of silk parallels engineered composite materials.

Protein Folding and Structure Types

Proteins can be categorized into fibrous, globular, and membrane proteins.
Fibrous proteins have parallel chains and are mechanically strong, often serving structural roles (e.g., keratins in hair and nails).
α-keratins are primarily composed of α-helical segments, forming coiled coils that aggregate into layered structures.

Oligomeric Proteins and Function

Oligomeric association allows proteins to be genetically economical, requiring less DNA for coding.
Monomeric proteins like HIV protease derive function from subunit interactions.
Cooperative binding is evident when ligand binding at one site alters the affinity at other sites, indicating allosteric influence.

Conformational Changes

Structural shifts in proteins can occur on nanosecond to microsecond timescales, driven by environmental stimuli or internal interactions.
Proline residues can undergo cis-trans isomerization, functioning as regulatory switches within proteins.

Importance of Protein Domains

Proteins adopt complex tertiary structures, exhibiting right-handed twists that enhance stability.
A common structural motif is the TIM barrel, featuring alternating α-helices and β-strands forming a barrel-like structure.
Similar structures may perform distinct functions, indicating that the relationship between structure and function is not always straightforward.

Molecular Chaperones

Molecular chaperones are vital for correct protein folding and preventing undesired interactions during synthesis and transport.
Heat shock proteins (Hsp) are induced in response to stress and assist in protein assembly.
Hsp70 and chaperonins (Cpn60s or Hsp60s), such as GroEL, are critical classes of chaperones facilitating protein folding.

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Description

Explore the elements of secondary structures in proteins, focusing on the formation of alpha-helices and the importance of hydrogen bonds. Understand how local conformations stabilize polypeptides and their cooperative nature in protein frameworks.