Chapter 4 Protein Three-Dimensional Structure

When a peptide bond is formed between two amino acids, a(n) ____________molecule is lost. A) Water B) Carbon dioxide C) Ammonia D) Hydrogen E) Oxygen

A) Water Explanation: Water is the correct answer because during the formation of a peptide bond (a type of condensation reaction), the carboxyl group of one amino acid reacts with the amino group of another. This reaction results in the release of a water molecule, with the hydrogen coming from the amino group and the hydroxyl from the carboxyl group, forming the peptide bond. This process is key to the synthesis of proteins from amino acids.

What determines a protein's function? A) its structure B) its gene sequence C) N-terminal amino acids D) None of the above. E) All of the above.

A) its structure Section: Introduction

How does a protein's amino acid sequence influence the tertiary structure?

A protein will spontaneously fold into a three-dimensional structure determined by the amino acid sequence. Section : Introduction

According to convention, ____________ is the terminus drawn on the left side of a peptide. A) Amino B) Carboxyl C) N-terminal D) C-terminal E) Alpha-terminal

A) Amino Explanation: The amino terminus, often referred to simply as the "amino" end, is conventionally drawn on the left side in peptide representations. This convention reflects the way proteins are synthesized in cells, from the N-terminus (amino terminus) to the C-terminus (carboxyl terminus). This directionality is crucial for understanding protein structure, function, and synthesis.

Two amino acids undergo oxidation to form a dimer called ____________. What is the name of the dimer formed by the oxidation of two cysteine molecules? A) Cystine B) Methionine C) Lysine D) Leucine E) Arginine

A) Cystine Explanation: Cystine is the correct answer because it is the dimer formed by the oxidation of two cysteine amino acids. This reaction involves the formation of a disulfide bond between the thiol groups of each cysteine. The resulting cystine molecule plays a critical role in stabilizing the structure of proteins by forming disulfide bridges that help maintain their three-dimensional shape. The other amino acids listed do not form dimers through similar oxidation processes.

____________: Compact regions that may be connected by a flexible segment of polypeptide chain. A) Domain B) Motif C) Helix D) Loop E) Segment

A) Domain Explanation: Domain is the correct answer because it refers to specific, compact, structurally independent parts of a protein that are often responsible for a particular function or interaction. Domains are typically connected by flexible segments of the polypeptide chain, which allow for movement and interaction between different parts of the protein. This structural feature is crucial for the modular assembly and function of many proteins. Motifs, helices, and loops are components of protein structures but do not encapsulate the concept of structural and functional independence as domains do.

______: This amino acid residue disrupts the α helix because its side chain contains a unique ring structure that restricts bond rotations. Which amino acid best completes this sentence and is known for its role in disrupting helical structures? A) Proline B) Phenylalanine C) Tyrosine D) Tryptophan E) Glycine

A) Proline Explanation: Proline is the correct answer because it has a unique ring structure that links the amino group to the side chain, creating a rigid structure that limits the flexibility of the polypeptide chain. This rigidity significantly disrupts the formation of α helices and β sheets due to the inability of the backbone to conform to the necessary angles for stable helix formation. Proline is often found at the turns or loops of proteins where flexibility is less critical, and its presence can even induce bends in the protein structure.

The plot that allows one to investigate the likely orientation of certain amino acid pairs is called the ____________. What is the name of the plot used for this purpose in protein structure analysis? A) Ramachandran plot B) Lineweaver-Burk plot C) Michaelis-Menten plot D) Scatchard plot E) Hill plot

A) Ramachandran plot Explanation: The Ramachandran plot is the correct answer because it is specifically used to visualize the dihedral angles ψ against φ of amino acid residues in protein structure. This plot helps in understanding the conformational angles allowed or favored for backbone atoms in protein secondary structures and thus is critical for predicting the likely orientation of amino acid pairs and assessing the feasibility of molecular conformations in proteins. The other plots listed are used in enzyme kinetics and binding studies, not in structural orientation analysis of proteins.

Why is the peptide bond planar? A) Bulky side chains prevent free rotation around the bond. B) It exhibits partial double-bond character, preventing rotation. C) Hydrogen bonding between the NH and C=O groups limits movement. D) None of the above. E) All of the above.

B The reason why peptide bonds are planar, or flat, is because they exhibit partial double-bond character, which restricts rotation around the bond. Peptide Bond Characteristics: Structure: A peptide bond is formed between the carboxyl group of one amino acid and the amine group of another, releasing water in a dehydration reaction. This results in a bond between the carbonyl carbon and the nitrogen. Resonance: The peptide bond has a unique feature called resonance, where electrons are shared between the oxygen, carbon, and nitrogen atoms. This electron sharing leads to the formation of a partial double bond. Partial Double-Bond Character: Impact on Rotation: Double bonds are generally rigid and do not allow for free rotation. Similarly, the partial double-bond nature of the peptide bond significantly restricts rotation around the bond. Planarity: As a result, the atoms involved in the peptide bond (C, O, N, and the attached H) generally lie in a flat, or planar, configuration. This planarity is essential for the overall structure of proteins and influences how the polypeptide chain can fold.

____________: Codes for the sequence of amino acids. A) RNA B) DNA C) mRNA D) tRNA E) rRNA

B) DNA Explanation: DNA is the correct answer because it contains the genetic instructions used in the development and functioning of all known living organisms and many viruses. These instructions are encoded in the DNA sequence, which determines the sequence of amino acids in proteins. RNA , mRNA, tRNA, and rRNA play crucial roles in the process of translating these instructions into proteins, but DNA is the original source of the genetic code

Changes in ____________ create amyloid fibers, which are insoluble and are the source of mad cow disease, Alzheimer disease, and Parkinson disease. A) Primary structure B) Secondary structure C) Tertiary structure D) Quaternary structure E) Protein sequencing

B) Secondary structure Explanation: Secondary structure is the correct answer because amyloid fibers form as a result of misfolding primarily at this level of protein structure. This misfolding often involves changes from α-helices to β-sheets, which aggregate into the insoluble fibers associated with various neurodegenerative diseases. These structural changes disrupt normal cellular functions and lead to the symptoms observed in diseases like mad cow disease, Alzheimer's, and Parkinson's. The primary, tertiary, and quaternary structures also play roles in protein function, but the critical amyloidogenic alterations occur at the secondary structure level.

____________: The type of structure to which α helices, β sheets, and turns are referred. Which term best completes this sentence and identifies the classification of these elements within a protein's architecture? A) Primary structure B) Secondary structure C) Tertiary structure D) Quaternary structure E) Super secondary structure

B) Secondary structure Explanation: Secondary structure is the correct answer because it specifically refers to local conformations of the polypeptide backbone, such as α helices and β sheets, which are stabilized by hydrogen bonds between backbone atoms. Turns are also considered part of secondary structure as they facilitate the folding and orientation necessary for the overall 3D structure of the protein. Primary structure deals with the linear sequence of amino acids, Tertiary structure involves the overall three-dimensional folding of a single protein molecule Quaternary structure pertains to the assembly of multiple protein subunits.

Which of the following amino acid residues would most likely be buried in the interior of a water-soluble, globular protein? A) aspartate B) serine C) phenylalanine D) lysine E) glutamine

C Section 4.3 Hydrophobic (water-repelling) amino acids tend to be buried inside the protein to avoid contact with water, while hydrophilic (water-attracting) amino acids are more likely to be on the exterior, interacting with the aqueous environment. Analysis of Amino Acid Residues: Aspartate (A) - A negatively charged, hydrophilic amino acid due to its carboxylate group. Likely to be on the protein surface. Serine (B) - Contains a polar hydroxyl group, making it hydrophilic and typically found on the protein surface. Phenylalanine (C) - A nonpolar, hydrophobic amino acid with a bulky aromatic side chain. This characteristic makes it likely to be buried within the protein to avoid water. Lysine (D) - Positively charged and hydrophilic, lysine's side chain often interacts with the aqueous environment, placing it on the exterior of proteins. Glutamine (E) - Although it has a polar amide group, it's less hydrophilic than amino acids like aspartate or serine and can sometimes be found in the interior, but it's more hydrophilic than phenylalanine.

What is the approximate mass of a protein containing 200 amino acids? (Assume there are no other protein modifications.) A) 20,000 B) 11,000 C) 22,000 D) 222,000 E) None of the above.

C) 22,000 Section 4.1 Calculation: Average Mass of an Amino Acid: Each amino acid in a protein has an average molecular weight of about 110 Daltons (or 110 g/mol). Total Mass of the Protein: For a protein with 200 amino acids, the total molecular weight is calculated by multiplying the number of amino acids by the average molecular weight per amino acid. Total Mass=200 amino acids×110 g/mol=22,000 g/molTotal Mass=200amino acids×110g/mol=22,000g/mol This means that the molecular weight of a protein with 200 amino acids, without considering any post-translational modifications, is approximately 22,000 Daltons. Answer: Correct Option: Based on the calculation, the correct answer is C) 22,000. Conclusion: In conclusion, the approximate mass of a protein consisting of 200 amino acids, assuming an average molecular weight of 110 Daltons per amino acid, is about 22,000 Daltons. This estimate provides a useful guideline for understanding the size and scale of proteins in molecular biology.

The overall 3D-structure of a single polypeptide chain is referred to as ____________. A) Primary structure B) Secondary structure C) Tertiary structure D) Quaternary structure E) Supersecondary structure

C) Tertiary structure Explanation: Tertiary structure is the correct answer because it describes the overall three-dimensional folding of a single polypeptide chain. This structure is stabilized by various interactions such as hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges between amino acid side chains. Tertiary structure is critical for the functional properties of the protein. In contrast, primary structure refers to the sequence of amino acids, secondary structure to the local conformations like α helices and β sheets, and quaternary structure to the assembly of multiple polypeptide subunits.

_________is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.

Collagen Section 4.3

The configuration of most α-carbon atoms of amino acids linked in a peptide bond is: A) cis. B) circular. C) parallel. D) trans. E) perpendicular.

D

Your study group is trying to identify differences in the four levels of protein structure. Which of the following would you say is true of important stabilizing forces in secondary structure but not tertiary structure? A) The structure is stabilized by ionic attractions between oppositely charged side chains. B) The structure is stabilized by H-bonding between polar side chains. C) The structure is stabilized by hydrophobic interactions between nonpolar side chains. D) The structure is stabilized by H-bonding between the oxygen of the backbone carbonyl and the hydrogen of the backbone amine. E) None of these differentiate between secondary and tertiary structure.

D Section 4.2 and Section 4.3 A) Ionic Attractions: Both secondary (less common) and tertiary structures can feature ionic attractions, but more typically among side chains in tertiary structures. B) H-bonding Between Polar Side Chains: This is more a feature of tertiary structure where side chains play a significant role in stabilization. C) Hydrophobic Interactions: Common in both secondary (within the context of folding) and tertiary structures, especially in stabilizing the folded form by aggregating nonpolar side chains internally. D) H-bonding Between Backbone Atoms: Correct Answer. This type of hydrogen bonding is characteristic and unique to secondary structures like α-helices and β-sheets, where it occurs regularly between the backbone carbonyl and amine groups, independent of side chain characteristics. E) None of These Differentiate: This would be incorrect given the unique role of backbone hydrogen bonding in secondary structures. Conclusion: The correct answer, D, highlights a specific and distinctive feature of secondary structure stabilization: hydrogen bonds that form directly between the main chain's carbonyl oxygen and amine hydrogen. This type of stabilization is not a primary characteristic of tertiary structure, which relies more on diverse interactions involving the side chains. This clear distinction makes D the best answer to the question regarding differences in stabilizing forces between secondary and tertiary protein structures.

Where are β turns and loops often found? A) in a hydrophobic pocket B) on the interior cleft C) at the protein interface with ligand D) on the surface of proteins E) None of the above.

D Section 4.3 β turns and loops are small, flexible regions of a protein that connect more structured elements like α helices and β sheets. Characteristics of β Turns and Loops: Flexibility: β turns and loops are highly flexible parts of the protein structure. This flexibility allows them to serve as connectors that enable the protein to fold into its functional three-dimensional shape. Composition: These regions often contain amino acids that are more polar or charged, which can interact favorably with the aqueous environment. Location in Protein Structure: On the Surface of Proteins (D): Because of their flexibility and the presence of polar or charged residues, β turns and loops are typically found on the surface of proteins. This external placement allows them to interact with the water molecules in the environment, which is essential for maintaining protein stability and function. Functional Roles: Interactions: Surface loops and turns can play critical roles in binding ligands or interacting with other proteins, due to their accessibility and adaptability. Dynamics: Their dynamic nature also makes them key sites for regulatory processes, where slight conformational changes can significantly impact the protein's activity. Conclusion: β turns and loops are often found on the surface of proteins (Answer D). This placement allows them to engage in interactions with the aqueous environment and other biological molecules, which is vital for the protein's functional and structural roles.

All of the following would disrupt quaternary structure except: A) increase the temperature B) decrease the pH. C) add 8 m Urea. D) treat with ascorbic acid (vitamin C). E) treat with β-mercaptoethanol.

D Section 4.4 A) Increase the temperature. Effect: Higher temperatures can cause protein denaturation by disrupting the weak interactions holding the subunits together. B) Decrease the pH. Effect: Changing pH can alter the charges on amino acid side chains, affecting ionic bonds and overall stability of the protein structure. C) Add 8 M Urea. Effect: Urea is a powerful denaturant that disrupts hydrogen bonding and other non-covalent interactions, leading to protein unfolding and disassembly of subunits. D) Treat with ascorbic acid (vitamin C). Effect: Ascorbic acid is a reducing agent and an essential cofactor in the hydroxylation of proline and lysine in collagen synthesis. In the context of non-collagenous proteins, it typically does not disrupt protein structures and may even aid in maintaining proper function and stability. E) Treat with β-mercaptoethanol. Effect: This compound breaks disulfide bonds, which can be crucial for stabilizing the quaternary structure in proteins that rely on these covalent bonds to maintain the assembly of their subunits. Conclusion: The question asks which treatment would not disrupt the quaternary structure. Among the listed treatments, D) Treat with ascorbic acid (vitamin C) is the least likely to cause disruption. It generally does not interfere with protein-protein interactions within quaternary structures, unless specific to a context where vitamin C's role as a cofactor alters protein conformation or stability (e.g., in collagen). In most typical biochemical scenarios, vitamin C does not disrupt protein structures and may support overall cellular health and enzymatic function. Thus, the correct answer is D, as it is the option least likely to disrupt quaternary structures of proteins unrelated to its specific cofactor roles.

The folding of a protein into its native shape can best be described as: A) a random event. B) a random event catalyzed by ribosome proteins to maintain a low energy structure. C) a series of controlled folds with a few random-shaped structures. D) a series of repeatable random events where the lowest energy structure is maintained. E) an event where the highest possible energy state is stabilized with discrete folding intermediates.

D Section 4.5 Protein Folding: Directed Process: While protein folding may seem random due to the number of potential conformations a polypeptide chain could theoretically adopt, it is actually a highly regulated and efficient process. Energy Landscape: Proteins fold into their native structure, which generally corresponds to the lowest free energy state. This process isn't random but guided by the protein's amino acid sequence and various intramolecular interactions. Explanation of Answer D: Repeatable Random Events: The phrase "repeatable random events" captures the idea that while the specific path a protein may take to reach its final structure can vary (each fold can occur in slightly different ways), the overall process consistently leads to the same low-energy native structure. Lowest Energy Structure Maintained: The stability of the native conformation is due to it being at the lowest energy state, which is thermodynamically favorable. This state minimizes the internal energy of the protein, balancing forces such as hydrophobic interactions, hydrogen bonds, ionic interactions, and van der Waals forces. Conclusion: Protein folding can be described as a series of processes where, despite the appearance of randomness in the path taken, the outcome—a stable, low-energy native structure—is consistently achieved. This description underscores the protein's ability to find and maintain its functional form in a complex cellular environment, guided by its inherent chemical and physical properties. Thus, the correct answer, D, emphasizes that while the pathways can vary (random events), the outcome (lowest energy structure) is predictable and repeatable.

The metamorphic protein lymphotactin undergoes changes in ___________ structure in order to carry out its full biochemical activity? A) primary and therefore also tertiary B) primary, secondary, and tertiary C) quaternary (subunits separate and carry out individual activities) D) secondary and tertiary E) primary, secondary, tertiary, and quaternary

D Section 4.5 Metamorphic proteins like lymphotactin have the unique ability to switch between different structures to carry out their functions. This ability is critical to their biological roles, allowing them to adapt to different cellular environments or signaling needs. Understanding Protein Structures: Primary Structure: The sequence of amino acids in a protein chain. Secondary Structure: Localized conformations of the peptide chain, including α-helices and β-sheets. Tertiary Structure: The overall three-dimensional shape of a single protein molecule. Quaternary Structure: The assembly of multiple protein subunits. Lymphotactin Structure Changes: Lymphotactin: This protein exhibits a remarkable ability to change its conformation. Specifically, it can alter its secondary and tertiary structures in response to different stimuli or environmental conditions. Changes Involved: Secondary Structure: Modifications in the folding patterns such as helices and sheets. Tertiary Structure: Overall changes in the 3D conformation of the protein, affecting how it interacts with other molecules or receptors. Explanation of the Correct Answer: D) Secondary and Tertiary: The correct answer highlights that lymphotactin undergoes changes in its secondary and tertiary structures. These changes are crucial for its ability to function in various biological contexts, allowing it to adapt its binding sites and interaction surfaces as needed for its activity. Conclusion: Metamorphic proteins like lymphotactin do not typically alter their primary sequence (amino acid order) or necessarily involve changes in quaternary structure (unless specifically part of their function).

What structure(s) did Pauling and Corey predict in 1951? A) α helix B) β sheet C) β turn D) A, B, and C E) A and B

E α helix β sheet Section 4.2

Which of the following protein(s) contain examples of α-helical character? A) keratin B) ferritin C) myosin D) tropomyosin E) All of the above.

E Section 4.2

A clinician friend comes to you and tells you she has a patient that she thinks has some sort of defect in the collagen structure. She wants to know what kinds of structural differences there might be. Which of the following is NOT true for defects leading to scurvy or brittle bone disease? A) Proline residues are not hydroxylated. B) Glycine is replaced by other amino acids C) Proyloyl hydroxylase activity is deficient. D) Accumulation of defective collagen causes cell death. E) All of the above are true.

E Section 4.2 Collagen is a critical structural protein in connective tissues, and its integrity depends on several post-translational modifications and the precise sequence of amino acids. Analysis of Each Option: A) Proline residues are not hydroxylated. Impact: Hydroxylation of proline residues in collagen is crucial for stabilizing the triple helix structure through hydrogen bonding. A lack of hydroxylation (common in vitamin C deficiency, which leads to scurvy) weakens collagen fibers. B) Glycine is replaced by other amino acids. Impact: Glycine, being the smallest amino acid, fits into the tight spaces of the collagen triple helix. Replacing glycine with bulkier amino acids can disrupt the helix, leading to conditions like brittle bone disease. C) Prolyl hydroxylase activity is deficient. Impact: Prolyl hydroxylase is an enzyme responsible for the hydroxylation of proline residues in collagen. Deficiency can lead to less stable collagen, similar to the effects seen in scurvy. D) Accumulation of defective collagen causes cell death. Impact: While defective collagen can lead to structural weaknesses and clinical symptoms, the direct causation of cell death solely by the accumulation of defective collagen is less straightforward. Structural issues and mechanical failures are more direct outcomes; cell death might not be a primary consequence but a secondary effect in severe cases.

Which of the following secondary structures would you expect to find on the surface of a globular protein? A) α helix B) β sheet C) loops between two α-helices D) none of the above because water would disrupt the hydrogen bonding that stabilizes these structures E) A, B, and C as long as the polar and charged amino acid side chains face the surface of the protein

E Section 4.2 Understanding Secondary Structures: α-Helix: This structure is stabilized by hydrogen bonds between the backbone carbonyl oxygen and the amide hydrogen four residues away. It can be surface-exposed if polar or charged residues are present on the exterior side of the helix. β-Sheet: Composed of β-strands linked laterally by two or more hydrogen bonds forming a sheet-like array. β-Sheets can be either parallel or antiparallel and are often found in both core and surface of proteins depending on side chain properties. Loops: These are flexible, non-repetitive regions that link other secondary structures like helices or sheets. Loops are often found on the protein surface because they can accommodate polar and charged residues that interact favorably with the aqueous environment. Location of Secondary Structures: The placement of these structures on the surface or interior of a protein is influenced by the side chain characteristics of the amino acids that compose them. Hydrophobic amino acids typically drive the structure towards the interior, while hydrophilic and charged side chains facilitate exposure on the surface. Misconceptions: D) None of the above: This option incorrectly suggests that water disrupts hydrogen bonding. In reality, the hydrogen bonding referred to stabilizes internal patterns within these structures and does not preclude their surface location. External hydrogen bonding with water can also occur, particularly with polar side chains.

Key properties of proteins include: A) a wide range of functional groups. B) an ability to possess either rigid or flexible structures as dictated by functional requirements. C) the ability to interact with other proteins. D) A and B. E) All of the above.

E) All of the above. Section 4.1

What is the sequence of amino acids found in collagen? What is the significance of the sequence and what is the complication of scurvy?

Gly-Pro-Pro. The small side group of the glycine allows for a tight screw turn for this atypical helix. The prolines are important to stabilize tight three-amino-acid helices. In addition, the prolines are also hydroxylated by an enzyme that requires ascorbic acid to maintain activity. Without the hydroxylation of collagen by prolylhydroxylase, the collagen superstructure is less stable and results in adverse flexibility of the connective tissues (scurvy).

What is the advantage of having certain regions of partially correct folded regions?

If some regions interact preferentially, lending stability to certain conformations as the protein folds, they can impact the overall structure of the protein. The concept of having certain regions of a protein fold partially or adopt preferential interactions before the protein fully folds is an important aspect of protein biochemistry. Partially Correct Folded Regions: Partial Folding: Some regions within a protein may fold into their correct or near-correct shapes earlier in the folding process. These regions can act as nuclei for further folding, guiding the rest of the protein toward its correct three-dimensional structure. Advantages: Stability and Speed: Folding Nuclei: These partially folded regions can stabilize certain conformations of the protein as it folds, reducing the number of incorrect folding pathways the protein might otherwise explore. This not only speeds up the folding process but also increases its efficiency. Energy Landscape: They help in smoothing the energy landscape, a conceptual model used to describe protein folding. By providing stable intermediates, they create a pathway that the protein can follow to reach its fully folded, functional state more easily and quickly. Correct Folding Guidance: Structural Templates: These regions serve as templates or scaffolds that guide other parts of the protein to fold correctly. They can help in correctly positioning other regions of the protein, particularly in large or complex proteins where correct folding is critical for function. Reduction of Misfolding: By establishing parts of the final structure early in the folding process, these regions can prevent misfolding and aggregation that might occur if the entire protein were to try to fold simultaneously.

Prion diseases are often latent; that is, those with prion diseases are asymptomatic for many years after their initial infection. What causes this latency?

Prion diseases are protein based; more specifically, protein-structure based. Because it takes time to convert the prion protein from the soluble, mostly helical form to the beta-strand, insoluble form, there is lag time before enough proteins are converted to the polymer, which causes cell injury This characteristic of prion diseases makes it difficult to diagnose before it is too late. Nature of Prions: Prions: These are misfolded forms of a normal protein called prion protein (PrP). Unlike bacteria or viruses, prions do not contain genetic material. They cause disease by inducing other normally folded proteins to adopt their misfolded prion form. Causes of Latency: Accumulation: Slow Buildup: The misfolded prion proteins accumulate very slowly in the nervous system. This slow accumulation is partly due to the stable nature of the prion protein, which resists breakdown. Threshold Effect: There is often a threshold amount of prion proteins that must accumulate before they start disrupting normal cellular processes significantly enough to cause symptoms. Propagation Rate: Cell-to-Cell Transmission: Misfolded prions propagate by converting normal proteins into the prion form. This conversion process can be slow and inefficient, leading to a gradual increase in prion numbers over time. Biochemical Stability: Resilience to Degradation: Prions are unusually resistant to the body's normal protein degradation mechanisms, which means they can persist and accumulate in tissues over long periods. Absence of Immune Response: Non-Recognition: Since prions are composed of host proteins albeit misfolded, they do not trigger an immune response. This lack of immune recognition allows prions to accumulate silently without being attacked or cleared by the immune system.

What are prions?

Prions are proteins that can assume (after infection or by other causes) a new protein structure that is self-propagating. Prion diseases have several variants, at least one of which is fatal to humans.

__________ refers to the spatial arrangement of subunits and the nature of their interactions.

Quaternary structure Section 4.4

Why are all the theoretical combinations of phi and psi not possible?

Steric hindrances of the side chains make certain combinations and angles impossible. Section: 4.2

How does the protein backbone add to structural stability?

The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) groups. Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the protein conformation. Section: 4.2

In the ribonuclease experiments performed by Anfinsen, what was the significance of the presence of the reducing agent β-mercaptoethanol?

The reducing agent reduced incorrectly paired disulfide bonds, allowing them to reform with the correct pairing until the most stable conformation of the protein had been obtained.

What are the key characteristics that make the peptide bond important to protein folding/structure?

The resonance of the amide bond creates a planar, rigid region of the peptide backbone with the R groups on opposite sides of the peptide bond. This results in a limit to the types and angles of conformation, allowing a predictable folding pattern.

Describe some of the features of an α helix.

The α helix is a coil stabilized by intrachain hydrogen bonds between the carbonyl oxygen of a residue and the amide hydrogen of the fourth residue away. There are 3.6 amino acids per turn. The hydrogen bonds are between amino acid residues that have two intervening residues. Thus, these amino acid residues are found on the same side of the coil. The helix is almost always right-handed, although left-handed helices are, in theory, possible.

A primary sequence of a protein contains a run of reasonably small amino acids, containing few branched amino acids or serines. This sequence ends in a proline. What can you deduce from this information?

The sequence is likely an α helix. The smaller amino acids do not sterically hinder the side groups on the outside of the helix and the absence of amino acids that would interfere with the helix are all evidence for this secondary structure. The proline is likely to be the end of the sequence. Small Amino Acids: The presence of small amino acids in a sequence suggests minimal steric hindrance, which facilitates tighter packing and more regular structures. Few Branched Amino Acids or Serines: Branched amino acids (like valine, leucine, and isoleucine) and serines can sometimes disrupt certain types of secondary structures due to steric bulk or the ability to form hydrogen bonds, respectively. Proline at the End: Proline is unique among amino acids due to its rigid ring structure, which limits the flexibility of the peptide backbone and can introduce a kink. Deduction of Secondary Structure: α-Helix Likelihood: Given the predominance of small amino acids and the absence of many branched amino acids or serines, the sequence is conducive to forming an α-helix. This type of secondary structure is characterized by a coiled arrangement where each turn of the coil is stabilized by hydrogen bonds between the backbone atoms of amino acids that are four residues apart. Role of Proline: The presence of proline at the end of the sequence is noteworthy. While proline is often a helix breaker when it occurs within an α-helix due to its inability to participate in standard backbone hydrogen bonding, its location at the end of this sequence suggests it may serve as a terminal residue that concludes the helical structure. Proline at the end might not disrupt the helix but rather signify its end, stabilizing the terminal turn of the helix.

What is the "hydrophobic effect" as it relates to protein structure?

The three-dimensional structure of a water-soluble protein is stabilized by the tendency of hydrophobic groups to assemble in the interior of the molecule. Basic Concept of the Hydrophobic Effect: Hydrophobicity: This refers to the tendency of nonpolar substances or molecular groups to avoid contact with water (hydrophilic) environments. In biological molecules such as proteins, hydrophobic groups are parts of the molecule that are not attracted to water and do not dissolve well in it. Role in Protein Structure: Protein Folding: When proteins fold, the hydrophobic effect plays a crucial role. The nonpolar (hydrophobic) side chains of amino acids tend to aggregate towards the interior of the protein, away from the aqueous environment (water). This aggregation reduces the surface area exposed to water, effectively "hiding" the hydrophobic groups from water. Stabilization: By minimizing their exposure to water, these hydrophobic groups help stabilize the overall structure of the protein. This configuration lowers the overall energy of the system, making the folded state of the protein thermodynamically favorable. Mechanism: Driving Force for Folding: The movement of hydrophobic groups away from water and towards the protein's interior is a major driving force in protein folding. This movement helps in compacting the protein into its functional form, influencing both the tertiary (overall 3D shape of a single protein molecule) and quaternary (assembly of multiple protein subunits) structures.

What is the advantage of protein interaction and assembly with other proteins?

When proteins interact or assemble, new functions and specificity become available. Protein interactions allow new binding sites at the assembly interface, and provide multifunctional activity and specificity, such as that found in polymerases and signal transduction. Section: Introduction

The secondary structure that is stabilized by CO and NH hydrogen bonding within the same contiguous peptide chain in a coiled configuration is the________.

alpha helix Section 4.2

The peptide bond is also known as a(n)________ .

amide bond Section 4.1 Peptide Bond: Formation: A peptide bond forms when the carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH2) of another amino acid. This reaction is a dehydration synthesis, where a molecule of water is removed as the bond forms. Structure: The resulting bond between the two amino acids is a covalent bond linking the carbonyl carbon of one amino acid to the nitrogen of the amino group of the adjacent amino acid. Amide Bond: Chemical Nature: In broader chemistry terms, an amide bond is formed between a carbonyl group (C=O) and a nitrogen atom (N) from an amine. This type of bond is characteristic of the amide functional group. Peptide as Amide: In the context of proteins, each peptide bond is essentially an amide bond because it involves this same linkage between a carbonyl carbon and a nitrogen atom. Importance in Proteins: Stability: Peptide (or amide) bonds are quite stable under physiological conditions, contributing to the structural integrity of proteins. Backbone Structure: These bonds form the backbone of the protein chain, crucial for the formation of the protein's primary structure and influencing higher levels of structure (secondary, tertiary, and quaternary).

The _______________β-sheet structure occurs when the two strands are oriented in opposite directions (N →C).

antiparallel Section 4.2

A protein is considered to be __________ when it is converted into a randomly coiled structure without its normal activity.

denatured Section 4.5 A protein is considered to be denatured when it loses its normal three-dimensional structure Denaturation: Definition: Denaturation involves the unfolding and disorganization of a protein's structure into a more random or disordered form. This process disrupts the precise arrangement of amino acid sequences and the interactions (like hydrogen bonds, ionic bonds, and disulfide bridges) that maintain the protein's functional conformation. Causes of Denaturation: Heat: Increasing temperature can cause proteins to lose their structure as heat energy disrupts the weak bonds holding the structure together. Chemicals: Certain chemicals, like strong acids, bases, or organic solvents, can also denature proteins by altering the chemical environment that supports the protein's structure. Physical Agitation: Vigorous shaking or mixing can lead to structural damage due to mechanical forces. Consequences: Loss of Function: Since the function of a protein is intricately tied to its structure, denaturation typically results in a loss of activity. Enzymes lose their catalytic ability, and structural proteins might fail to maintain integrity. Reversibility: Denaturation can be reversible or irreversible depending on the extent of damage and the conditions leading to denaturation. Mild denaturation conditions may allow the protein to refold correctly once normal conditions are restored. Conclusion: In summary, a protein is termed denatured when it transforms into a randomly coiled structure without its characteristic biological activity due to disruption of its specific three-dimensional structure. This concept is crucial in understanding protein functionality and stability under varying environmental conditions.

Every third residue in the protein collagen is_________ .

glycine Section 4.2

Collagen contains________ , a modified amino acid.

hydroxyproline Section 4.3

The _______ of a disulfide bridge results in a separation of two protein chains.

oxidation Section 4.1 Disulfide Bridge: This is a covalent bond formed between two cysteine residues within a protein or between two different protein chains. The bond is between the sulfur atoms of the cysteine side chains. Oxidation and Reduction: Oxidation: In the context of disulfide bridges, oxidation refers to the formation of the disulfide bond. This involves the loss of hydrogen atoms from two thiol groups (-SH) on cysteine residues, resulting in the formation of a disulfide bond (-S-S-). Reduction: Conversely, the reduction of a disulfide bond refers to the breaking of the -S-S- link, with each sulfur atom regaining a hydrogen to reform the thiol groups (-SH). This process separates the linked cysteine residues or protein chains. Functional Impact: Structural Stability: The formation of disulfide bridges by oxidation often stabilizes the three-dimensional structure of proteins, particularly those secreted outside the cell where oxidative conditions are more prevalent. Separation and Flexibility: The reduction of these bridges (the reverse of oxidation) can lead to a separation of protein chains or domains, increasing the flexibility or changing the function of the protein. Conclusion: In summary, the oxidation of a disulfide bridge results in the formation of a bond that can link two chains of a protein, stabilizing its structure. Conversely, the reduction (breaking) of this bridge can separate these chains, which is critical for the functional regulation of some proteins under different physiological conditions.

The _____ _indicates the left- or right-handedness of an αhelix.

screw sense Section 4.2

Compact, globular proteins are typically water _______ and consist mostly of ____ _______secondary structure.

soluble; an alpha helical 4.3

Peptides differ from proteins in __________.

the number of amino acid residues Section 4.1 Peptides and proteins are both polymers of amino acids, but they differ primarily in the number of amino acid residues they contain. Peptides: Definition: Peptides are short chains of amino acids linked by peptide bonds. Size: Typically, peptides consist of anywhere from 2 to around 50 amino acids. Proteins: Definition: Proteins are longer chains of amino acids and are complex macromolecules with higher structural organization. Size: Generally, proteins are made up of 50 or more amino acids, often several hundreds. The larger size allows proteins to fold into specific three-dimensional structures necessary for their biological functions. Key Differences: Complexity and Function: Due to their size, proteins can fold into more complex structures than peptides, enabling them to perform a wide variety of functions in the body, including catalytic, structural, and regulatory roles. Peptides, being smaller, typically have fewer complex functions but are crucial in many biological processes, such as signaling, where their smaller size allows rapid synthesis and degradation. Terminology: In common scientific terminology, the transition from calling a chain of amino acids a peptide to calling it a protein often depends not only on the number of residues but also on the function and complexity of the molecule.

Due to the side chain steric clash, almost all peptide bonds are _______ in their configuration.

trans Section 4.1

________ is a fibrous protein and is the primary component of wool and hair.

α-keratin Section 4.2 α-Keratin: Type of Protein: α-Keratin is a type of fibrous protein, meaning it has a long, filamentous structure. Composition: It is composed of long chains of amino acids arranged into coils or helices, specifically alpha helices, which are twisted together like ropes. Properties and Function: Strength and Durability: The structure of α-keratin, with its coiled and twisted alpha helices, gives it remarkable strength and durability, which is ideal for the structural demands of hair and wool. Major Component: As the primary component of wool and hair, α-keratin provides these materials with their resilience and ability to withstand mechanical stress. Role in Hair and Wool: Protection and Structure: In hair and wool, α-keratin's structure allows for flexibility and strength, protecting the shaft of hair and fibers of wool against damage.

Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as___________ .

β-mecaptoethanol Section 4.5

A protein whose peptide backbone is mostly extended and hydrogen bonded to different strands of the protein is composed mostly of the__________secondary structure.

β-sheet Section 4.3