p.23
Protein Misfolding and Associated Diseases
Can the tertiary structure of a protein be altered?
Yes, changes in environmental conditions or mutations can lead to denaturation or misfolding.
p.39
Favorable Interactions in Protein Folding
What causes the sulfur-like smell when burning hair?
The Cys residues in keratin.
p.36
Fibrous vs. Globular Proteins
What are fibrous proteins primarily known for?
They are structural proteins.
p.15
Secondary Structure: Alpha Helices and Beta Sheets
What type of bonds stabilize β-sheets?
Hydrogen bonds between β-strands.
p.29
Methods for Protein Structural Determination
What is the second step in the Cryo-EM process?
Adhere the protein to a grid.
p.8
Protein Structure Overview
What do Ramachandran plots illustrate?
The allowed and disallowed combinations of Ramachandran angles in protein structures.
p.43
Favorable Interactions in Protein Folding
How do London dispersion interactions contribute to silk fibroin's structure?
They occur between sheets, helping to stabilize the overall structure.
p.3
Protein Folding Thermodynamics
What is the entropy cost associated with protein folding?
There is an entropy cost to folding the protein into one specific native fold.
p.50
Chaperones and Protein Folding Assistance
What role do chaperones play in protein life cycles?
They assist in the proper folding of proteins.
p.23
Protein Structure Overview
How does the tertiary structure affect protein function?
The specific shape of the protein determines its function and interaction with other molecules.
p.39
Favorable Interactions in Protein Folding
What is the role of disulfide linkages in curling hair?
They form alternate linkages to introduce waves.
p.57
Protein Folding Thermodynamics
What does Levinthal's paradox imply about the protein folding process?
It suggests that proteins cannot randomly sample all possible conformations due to the vast number of possibilities.
p.44
Fibrous vs. Globular Proteins
What are some functions of globular proteins?
Synthesizing, transporting, and metabolizing.
p.44
Levels of Protein Structure: Primary to Quaternary
What is the relationship between structure and function in proteins?
Structure determines function (structure-function relationship).
p.21
Secondary Structure: Alpha Helices and Beta Sheets
What do amino acids in secondary structural elements correspond to?
Defined regions of the Ramachandran plot.
p.15
Secondary Structure: Alpha Helices and Beta Sheets
How do hydrogen bonds affect β-sheets?
They stabilize the β-sheet structure.
p.50
Protein Structure Overview
What is the first step in the life cycle of a protein?
Synthesis of the protein from amino acids.
p.30
Methods for Protein Structural Determination
What is a potential benefit of using Cryo-EM?
It has the possibility of achieving high resolution.
p.25
Levels of Protein Structure: Primary to Quaternary
What is a characteristic feature of proteins in viruses with many subunits?
They have a regular structure of repeating units.
p.25
Methods for Protein Structural Determination
How are the structures of complex proteins in viruses determined?
Through crystallographic methods.
p.66
Chaperones and Protein Folding Assistance
What are chaperonins?
Proteins that provide a protective environment for other proteins to fold into their 3D structure.
p.17
Secondary Structure: Alpha Helices and Beta Sheets
How do alpha helices and beta sheets contribute to protein structure?
They provide stability and define the overall shape of the protein.
p.55
Anfinsen's Experiment and Protein Folding
What is the first step in Anfinsen's experiment?
Remove β - ME first, then remove urea.
p.11
Secondary Structure: Alpha Helices and Beta Sheets
What is the chirality of most amino acids?
Most amino acids have chirality, meaning they exist in two mirror-image forms.
p.43
Favorable Interactions in Protein Folding
What stabilizes the structure of silk fibroin?
Hydrogen bonding within sheets and London dispersion interactions between sheets.
p.30
Methods for Protein Structural Determination
What is a major advantage of Cryo-EM in protein structural determination?
It does not require crystallization.
p.8
Protein Folding Thermodynamics
What is a key observation regarding protein structures in Ramachandran plots?
The total number of possible structures is limited.
p.47
Protein Structure Overview
What does the transcription factor SATB1 illustrate?
It demonstrates motifs in protein structure, represented by green and blue.
p.50
Protein Misfolding and Associated Diseases
What can happen if a protein misfolds?
It can lead to loss of function or diseases.
p.1
Protein Folding Thermodynamics
What aspect of protein folding is covered in Part 2?
Thermodynamics and chaperones.
p.53
Protein Misfolding and Associated Diseases
What is denaturation of proteins?
The process of unfolding proteins, making them inactive.
p.63
Protein Folding Thermodynamics
What does 'folding is all or nothing' mean in protein folding?
It means that proteins either fold completely or not at all.
p.17
Favorable Interactions in Protein Folding
What role do side chains play in the assembly of secondary structures?
They influence the folding and stability of the secondary structures.
p.28
Methods for Protein Structural Determination
What is a significant disadvantage of X-ray crystallography?
It is difficult for membrane proteins.
p.35
Methods for Protein Structural Determination
What size subunit is indicated at 40 kDa?
It shows a smaller subunit in the complex.
p.49
Levels of Protein Structure: Primary to Quaternary
What is the difference between a subunit and a domain?
A subunit refers to different chains in a protein, while a domain refers to a distinct folding unit within the same chain.
p.64
Chaperones and Protein Folding Assistance
What is the function of Protein Disulfide Isomerase (PDI)?
It catalyzes the interchange of disulfide bonds until the native conformation is formed.
p.64
Chaperones and Protein Folding Assistance
What does Peptide Prolyl Cis-Trans Isomerase (PPI) do?
It catalyzes the interconversion of the cis and trans isomers of proline residues in peptide bonds.
p.40
Fibrous vs. Globular Proteins
What is collagen primarily a constituent of?
Connective tissue, including tendons, cartilage, bones, and the cornea of the eye.
p.4
Favorable Interactions in Protein Folding
What are van der Waals interactions?
Weak attractions between molecules that contribute to protein stability.
p.22
Levels of Protein Structure: Primary to Quaternary
What defines the tertiary structure of a protein?
The overall three-dimensional shape formed by the folding of a single polypeptide chain.
p.11
Secondary Structure: Alpha Helices and Beta Sheets
What is a right-handed helix?
A common structural form in proteins where the helix twists in a right-handed direction.
p.57
Protein Folding Thermodynamics
What is Levinthal's paradox?
It questions how proteins can find their correct fold given the vast number of possible conformations.
p.48
Levels of Protein Structure: Primary to Quaternary
What is a B motif?
A small part of a larger structure in proteins.
p.14
Secondary Structure: Alpha Helices and Beta Sheets
What is a β-strand?
A β-strand is a type of secondary structure in proteins characterized by a zigzag pattern of amino acids.
p.21
Secondary Structure: Alpha Helices and Beta Sheets
What are secondary structural elements in proteins associated with?
Distinct Ramachandran regions.
p.58
Secondary Structure: Alpha Helices and Beta Sheets
What forms as the protein folds?
Secondary structural elements.
p.3
Protein Structure Overview
What is the significance of a protein's native fold?
It fulfills a specific biological function.
p.8
Favorable Interactions in Protein Folding
What causes steric clashes in Ramachandran plots?
Certain combinations of Ramachandran angles, depending on the size of the side chain R-group.
p.32
Methods for Protein Structural Determination
What is the purpose of assigning signals in the NMR process?
To identify the different signals using computer-based methods.
p.45
Protein Structure Overview
What do X-helices display in protein structures?
They show where things are happening in the protein.
p.45
Protein Structure Overview
What do X-helices indicate about side chains?
They show where side chains are located.
p.34
Methods for Protein Structural Determination
What type of molecules can be analyzed using size exclusion chromatography?
Whole complexes and individual molecules.
p.49
Levels of Protein Structure: Primary to Quaternary
What is a domain in the context of proteins?
A portion of a polypeptide chain that folds on itself to form a compact unit, distinct within the tertiary structure.
p.35
Methods for Protein Structural Determination
What is the significance of size exclusion in SDS PAGE?
It allows separation of proteins based on their size.
p.33
Methods for Protein Structural Determination
What type of structures can Biomolecular NMR determine?
It can determine both secondary and quaternary structures.
p.53
Protein Folding Thermodynamics
What is the stability of a protein dependent on?
The proper folding of the protein.
p.9
Secondary Structure: Alpha Helices and Beta Sheets
What type of interactions are involved in the wrapping of residues in an alpha helix?
Interactions between the side chains of residues.
p.12
Secondary Structure: Alpha Helices and Beta Sheets
Which amino acid interactions can stabilize an α-helix?
R group interactions, specifically patterns like ① ⑦ ⑦ or RXXXRXXXEXXX.
p.12
Secondary Structure: Alpha Helices and Beta Sheets
What is the effect of the sequence 12345 on α-helix stability?
It destabilizes the α-helix.
p.12
Secondary Structure: Alpha Helices and Beta Sheets
Is the sequence 12345 considered a stable α-helix?
No, it's considered a bad helix.
p.61
Favorable Interactions in Protein Folding
What type of interactions fulfill more hydrogen bonding in proteins?
Hydrophilic interactions.
p.61
Favorable Interactions in Protein Folding
What is the role of clathrates in protein folding?
They are involved in the hydration shell around proteins.
p.2
Protein Structure Overview
What is protein structure?
The three-dimensional arrangement of atoms in a protein.
p.22
Levels of Protein Structure: Primary to Quaternary
What is the quaternary structure of a protein?
The arrangement of multiple polypeptide chains into a functional protein complex.
p.38
Favorable Interactions in Protein Folding
How do α-keratin chains maximize contact between hydrophobic surfaces?
By intertwining into a left-handed coiled-coil structure.
p.2
Levels of Protein Structure: Primary to Quaternary
What is the tertiary structure of a protein?
The overall three-dimensional shape of a single polypeptide chain.
p.41
Favorable Interactions in Protein Folding
What type of interactions help hold collagen in its spiral structure?
Non-covalent interactions.
p.51
Protein Misfolding and Associated Diseases
What can extreme conditions do to proteins?
Extreme conditions can lead to denaturation.
p.23
Chaperones and Protein Folding Assistance
What role do chaperones play in protein tertiary structure formation?
Chaperones assist in the proper folding of proteins into their tertiary structure.
p.42
Protein Structure Overview
What amino acids are involved in crosslinking in collagen?
Lysine (Lys), Hydroxylysine (OH-Lys), and Histidine (HIS).
p.48
Protein Structure Overview
What do repeated motifs contribute to in proteins?
Overall structure and folding.
p.6
Secondary Structure: Alpha Helices and Beta Sheets
What does a segment of the polypeptide chain describe in secondary structure?
The local arrangement of main-chain atoms.
p.29
Methods for Protein Structural Determination
What is done to the protein after it is adhered to the grid in Cryo-EM?
Freeze it in amorphous ice.
p.25
Protein Structure Overview
What type of interactions are observed in complex proteins of viruses?
Protein-protein interactions.
p.3
Favorable Interactions in Protein Folding
What role do disulfides play in protein structure?
They contribute to favorable interactions.
p.34
Methods for Protein Structural Determination
What is the purpose of size exclusion chromatography?
To estimate the size of molecules or complexes.
p.17
Secondary Structure: Alpha Helices and Beta Sheets
What are the main types of secondary structural elements in proteins?
Alpha helices and beta sheets.
p.1
Chaperones and Protein Folding Assistance
What role do chaperones play in protein folding?
They assist in the proper folding of proteins.
p.49
Levels of Protein Structure: Primary to Quaternary
What is a key characteristic of different domains in proteins?
Different domains often carry out different functions.
p.33
Methods for Protein Structural Determination
What is a limitation of Biomolecular NMR?
It requires the protein to be soluble.
p.46
Favorable Interactions in Protein Folding
How do globular proteins stabilize their structure?
Through hydrogen bonding and ionic interactions.
p.65
Chaperones and Protein Folding Assistance
What do HSPs prevent during the protein folding process?
They prevent hydrophobic regions from being exposed to the solvent.
p.65
Chaperones and Protein Folding Assistance
What analogy is used to describe the function of HSPs?
Using open teeth to close teeth, representing how they assist in proper folding.
p.4
Favorable Interactions in Protein Folding
What role do hydrophobic residues play in protein structure?
They lead to local structure formation.
p.60
Fibrous vs. Globular Proteins
What is the core characteristic of globular proteins?
They have a hydrophobic core.
p.38
Fibrous vs. Globular Proteins
What materials primarily consist of α-keratin?
Hair, wool, nails, claws, quills, horns, hooves, and the outer layer of skin.
p.41
Protein Structure Overview
What is the significance of Vitamin C in collagen synthesis?
It is essential for the activity of prolyl hydroxylase.
p.2
Levels of Protein Structure: Primary to Quaternary
What is quaternary structure in proteins?
The arrangement of multiple polypeptide chains into a single functional unit.
p.51
Protein Folding Thermodynamics
How does protein structure relate to its function?
The fold of a protein structure determines its function.
p.52
Protein Misfolding and Associated Diseases
How does Guanidinium HCl disrupt protein structure?
It interacts with negatively charged amino acids or hydrogen bonds, disrupting stabilizing H-bonds and salt bridges.
p.57
Protein Folding Thermodynamics
What is the total number of possible conformations for a protein with 100 residues and 10 conformations per residue?
10^100 possible conformations.
p.19
Secondary Structure: Alpha Helices and Beta Sheets
How are amino acids distributed among protein secondary structural elements?
Amino acids are unevenly distributed.
p.36
Fibrous vs. Globular Proteins
What is the main function of globular proteins?
They carry out biochemical functions.
p.43
Protein Structure Overview
What is fibroin?
The main protein in silk from moths and spiders.
p.58
Protein Folding Thermodynamics
What occurs as more elements start to fold in a protein?
More structural constraints are established.
p.50
Levels of Protein Structure: Primary to Quaternary
What happens after a protein is synthesized?
It undergoes folding to achieve its functional structure.
p.32
Methods for Protein Structural Determination
What is the final step in calculating the protein structure using NMR?
Calculate the structure based on the assigned signals.
p.54
Anfinsen's Experiment and Protein Folding
What is the primary factor that directs the folding of a protein?
The sequence of the protein.
p.5
Levels of Protein Structure: Primary to Quaternary
What is the role of amino acid sequences in proteins?
They dictate the protein's structure and function.
p.45
Protein Structure Overview
What are the two common modes of displaying proteins?
Cartoon depiction and space-filling models.
p.65
Chaperones and Protein Folding Assistance
What is the role of Heat Shock Proteins (HSPs) in protein folding?
HSPs help bind hydrophobic cores to prevent exposure to solvent.
p.65
Chaperones and Protein Folding Assistance
How do HSPs function in extreme temperature environments?
They assist in protein folding from really hot to really cold environments.
p.55
Anfinsen's Experiment and Protein Folding
What does adding BMG do in the context of Anfinsen's experiment?
It does not do what it needs to do.
p.26
Methods for Protein Structural Determination
What is significant about hemoglobin in terms of protein structure?
It was the first oligomeric protein whose structure was solved.
p.64
Chaperones and Protein Folding Assistance
What are the two main types of chaperones?
HSP70 or HSP40 and chaperonins.
p.13
Secondary Structure: Alpha Helices and Beta Sheets
What determines whether a residue is allowed in α-helices?
The difference in free energies reflects whether the inclusion of the residue stabilizes or destabilizes the helix.
p.40
Favorable Interactions in Protein Folding
How does the tensile strength of collagen compare to steel?
The triple helix has higher tensile strength than a steel wire of equal cross section.
p.41
Favorable Interactions in Protein Folding
How does hydroxyproline increase hydrogen bonding in collagen?
By adding a hydroxyl group (OH).
p.51
Protein Misfolding and Associated Diseases
What can cause a protein to unfold?
Denaturation can cause a protein to unfold.
p.23
Levels of Protein Structure: Primary to Quaternary
What is protein tertiary structure?
The three-dimensional shape of a protein formed by the folding of its polypeptide chain.
p.23
Favorable Interactions in Protein Folding
What interactions stabilize the tertiary structure of proteins?
Hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.
p.52
Protein Misfolding and Associated Diseases
What is the mode of action of strong acids/bases in disrupting protein tertiary structure?
They protonate/deprotonate charged residues, leading to loss of corresponding interactions.
p.52
Protein Misfolding and Associated Diseases
What is the effect of Urea on protein tertiary structure?
It forms hydrogen bonds with various groups, leading to destabilization.
p.52
Protein Misfolding and Associated Diseases
What does β-mercaptoethanol do to protein structure?
It reduces disulfide bonds, leading to disruption of structure.
p.42
Protein Structure Overview
What happens to Lys, OH-Lys, or HIS during collagen crosslinking?
They are oxidized to aldehyde.
p.68
Protein Misfolding and Associated Diseases
What are prions?
A type of protein misfolding disease.
p.31
Methods for Protein Structural Determination
What is an example of a protein studied using Cryo-EM?
SARS-CoV-2 spike protein.
p.31
Methods for Protein Structural Determination
What is a key advantage of using Cryo-EM for studying proteins?
Proteins do not need to be crystallized.
p.7
Protein Structure Overview
What is a polypeptide made up of?
A series of planes linked at α carbons.
p.7
Protein Structure Overview
What are α carbons in the context of polypeptides?
The central carbon atoms to which amino acids are attached.
p.6
Secondary Structure: Alpha Helices and Beta Sheets
What does the secondary protein structure refer to?
The 3D structure of the local amino acid backbone.
p.6
Secondary Structure: Alpha Helices and Beta Sheets
What is the focus when considering secondary structural elements?
The local arrangement, without regard to spatial relationships with other elements.
p.67
Protein Misfolding and Associated Diseases
What is often correlated with amyloid diseases?
Inherited genetic mutations that yield a destabilized protein variant.
p.43
Secondary Structure: Alpha Helices and Beta Sheets
What type of structure does silk fibroin have?
Antiparallel beta sheet structure.
p.6
Secondary Structure: Alpha Helices and Beta Sheets
What are the main types of secondary protein structures?
Alpha helix and beta sheet.
p.67
Protein Misfolding and Associated Diseases
What can stabilize the formation of amyloid fibrils?
Variants of proteins that stabilize the amyloid fibrils.
p.58
Favorable Interactions in Protein Folding
What happens to amino acid sidechains during protein folding?
They become increasingly more constrained to accommodate the structure.
p.43
Favorable Interactions in Protein Folding
Which amino acids contribute to the close packing of silk fibroin sheets?
Small side chains of Alanine (Ala) and Glycine (Gly).
p.32
Methods for Protein Structural Determination
What is the first step in the biomolecular NMR method for protein structural determination?
Ensure the purity of the protein.
p.5
Levels of Protein Structure: Primary to Quaternary
What is the primary structure of a protein?
The sequence of amino acids in a polypeptide chain.
p.30
Methods for Protein Structural Determination
What is a disadvantage of Cryo-EM for small proteins?
It is hard to use for small proteins.
p.30
Methods for Protein Structural Determination
What is a challenge associated with sample preparation in Cryo-EM?
It requires hands-on sample preparation.
p.30
Methods for Protein Structural Determination
What issue can arise with sample homogeneity in Cryo-EM?
There may be no homogeneity in the samples.
p.33
Methods for Protein Structural Determination
What is a major advantage of Biomolecular NMR in protein structural determination?
It does not require crystallization or freezing.
p.66
Chaperones and Protein Folding Assistance
What happens to proteins inside chaperonins?
They can fold properly into their functional 3D structures.
p.46
Protein Structure Overview
What characterizes the interiors of globular proteins?
They have hydrophobic interiors.
p.63
Protein Folding Thermodynamics
How does temperature affect protein unfolding?
Higher temperature can help unfold proteins more.
p.9
Secondary Structure: Alpha Helices and Beta Sheets
Where are the side chains of residues located in an alpha helix?
The side chains (R groups) are on the outside.
p.33
Methods for Protein Structural Determination
For which size of proteins does Biomolecular NMR work best?
It works best for smaller proteins.
p.16
Secondary Structure: Alpha Helices and Beta Sheets
What structural feature causes the 'pleats' in β-sheets?
The tetrahedral α-carbon in each residue.
p.10
Protein Structure Overview
What is Linus Pauling known for in relation to bond angles?
He proposed the concept of hybridization and defined specific bond angles for different molecular geometries.
p.61
Protein Folding Thermodynamics
Which state has higher disorder, unfolded or native fold?
The unfolded state has higher disorder.
p.22
Levels of Protein Structure: Primary to Quaternary
What characterizes the primary structure of a protein?
The sequence of amino acids in a polypeptide chain.
p.38
Protein Structure Overview
What is the structural form of each α-keratin chain?
A long right-handed helix with 3.6 residues per turn.
p.13
Secondary Structure: Alpha Helices and Beta Sheets
Why is proline not good in α-helices?
Proline is unfavorable due to its structure, which restricts rotation.
p.2
Secondary Structure: Alpha Helices and Beta Sheets
What is secondary structure in proteins?
Local folded structures that form within a protein due to hydrogen bonding, such as alpha helices and beta sheets.
p.56
Anfinsen's Experiment and Protein Folding
What did Anfinsen's experiments suggest about protein folding?
Proteins mostly fold to their minimum energy state.
p.51
Protein Misfolding and Associated Diseases
What are chemical agents' roles in protein stability?
Chemical agents can disrupt protein structure and lead to denaturation.
p.32
Methods for Protein Structural Determination
What is the second step in the NMR process for protein structural determination?
Dissolve the proteins in a suitable solvent (D2O).
p.5
Levels of Protein Structure: Primary to Quaternary
What does the sequence 'MRKGEELFTG VVPILVELDG DVNGHKFSVS GEGEGDATNG' represent?
A specific primary protein structure.
p.5
Levels of Protein Structure: Primary to Quaternary
What are the termini of a protein?
The N-terminus (amino end) and C-terminus (carboxyl end).
p.34
Methods for Protein Structural Determination
What can size exclusion chromatography help determine if you don't have a structure?
The size of the whole complex.
p.45
Protein Structure Overview
How do X-helices help in understanding protein interactions?
They illustrate how other things are interacting with the protein.
p.9
Secondary Structure: Alpha Helices and Beta Sheets
How many residues are typically found in one turn of an alpha helix?
Approximately 3.6 residues.
p.24
Levels of Protein Structure: Primary to Quaternary
What is the quaternary structure of human insulin?
Human insulin consists of two chains, A and B, linked by disulfide bonds.
p.63
Protein Folding Thermodynamics
What does an increase in Tm indicate?
It indicates a higher melting temperature, suggesting more stability in the folded state.
p.62
Protein Folding Thermodynamics
What are the two states of protein structure mentioned?
Denatured (unfolded) and native (folded).
p.62
Protein Folding Thermodynamics
What happens during the folding process in terms of energy?
Folding requires energy but can still be unfavorable.
p.10
Protein Structure Overview
What are the typical bond angles for a tetrahedral geometry?
Approximately 109.5 degrees.
p.4
Favorable Interactions in Protein Folding
What is a salt bridge in the context of proteins?
An interaction between charged residues that stabilizes protein structure.
p.22
Secondary Structure: Alpha Helices and Beta Sheets
What is the secondary structure of a protein?
The local folding of the polypeptide chain into alpha helices and beta sheets.
p.60
Fibrous vs. Globular Proteins
How do the hydrophobic and hydrophilic regions of globular proteins interact with water?
Hydrophobic regions are shielded from water, while hydrophilic regions interact with water.
p.10
Protein Structure Overview
What is the significance of bond lengths in molecular structure?
Bond lengths influence the stability and reactivity of molecules.
p.18
Protein Structure Overview
What is unique about proline compared to other amino acids?
Proline is a cyclic amino acid, which means it has a unique ring structure.
p.56
Anfinsen's Experiment and Protein Folding
What must be true about thiol groups prior to reoxidation in Anfinsen's experiments?
They must have been adjacent to each other due to correct backbone refolding.
p.18
Protein Folding Thermodynamics
How does the cyclic structure of proline affect its conformation?
It restricts the rotation around the N-Cα bond, influencing the overall protein structure.
p.51
Protein Misfolding and Associated Diseases
How does changing the solvent from water to an organic solvent affect proteins?
It can lead to denaturation of proteins.
p.3
Favorable Interactions in Protein Folding
What type of interactions are present in the native fold of a protein?
A large number of favorable interactions within the protein.
p.47
Protein Structure Overview
What is a motif in protein structure?
A recognizable folding pattern involving two or more elements of secondary structure and the connections between them.
p.1
Levels of Protein Structure: Primary to Quaternary
What are the levels of protein structure discussed in Chapter 4?
2° (secondary), 3° (tertiary), and 4° (quaternary) structure.
p.1
Fibrous vs. Globular Proteins
What are the two main types of proteins mentioned?
Fibrous and globular proteins.
p.46
Protein Structure Overview
What is a common feature of all globular proteins?
They have a compact fold.
p.17
Favorable Interactions in Protein Folding
What interactions stabilize secondary structures in proteins?
Hydrogen bonds between the backbone amide and carbonyl groups.
p.55
Anfinsen's Experiment and Protein Folding
What happens when urea is removed first in Anfinsen's experiment?
It destabilizes H-bonding.
p.53
Protein Folding Thermodynamics
Can denatured proteins sometimes fold back?
Yes, sometimes they can renature (fold back).
p.17
Levels of Protein Structure: Primary to Quaternary
How are secondary structural elements arranged in a protein?
They are organized into motifs and domains that contribute to the protein's overall architecture.
p.12
Secondary Structure: Alpha Helices and Beta Sheets
What stabilizes an α-helix?
Internal hydrogen bonding between the backbone atoms.
p.59
Protein Folding Thermodynamics
What happens to entropy during protein folding?
It decreases, which is considered unfavorable.
p.16
Secondary Structure: Alpha Helices and Beta Sheets
What is the significance of the bond interactions in β-sheets compared to α-helices?
The bond interactions in β-sheets are less than those in α-helices.
p.40
Protein Structure Overview
What is the structure of each collagen chain?
A long Gly-Pro-rich left-handed helix with 4-hydroxyproline.
p.61
Favorable Interactions in Protein Folding
What is the difference between hydrophobic and hydrophilic regions in proteins?
Hydrophobic regions avoid water, while hydrophilic regions interact with water.
p.37
Fibrous vs. Globular Proteins
What is the structure of α-Keratin?
α Helix, cross-linked by disulfide bonds.
p.60
Fibrous vs. Globular Proteins
Where do hydrophilic residues typically point in globular proteins?
Outward, towards the surrounding water.
p.13
Secondary Structure: Alpha Helices and Beta Sheets
How does alanine compare to proline and glycine in terms of stability in α-helices?
Alanine is more stable compared to proline and glycine.
p.37
Fibrous vs. Globular Proteins
Where is collagen found?
In tendons and bone matrix.
p.51
Favorable Interactions in Protein Folding
What are salt bridges in the context of protein stability?
Salt bridges are interactions that stabilize protein structure.
p.50
Favorable Interactions in Protein Folding
What is crucial for proper protein folding?
The sequence of amino acids and environmental conditions.
p.5
Levels of Protein Structure: Primary to Quaternary
What is the significance of the N-terminus and C-terminus in proteins?
They determine the directionality of the polypeptide chain.
p.66
Chaperones and Protein Folding Assistance
What is the main function of chaperonins?
To assist proteins in achieving their correct 3D structure after folding.
p.49
Levels of Protein Structure: Primary to Quaternary
How do large proteins typically relate to domains?
Large proteins often consist of several domains.
p.59
Protein Folding Thermodynamics
What are the two states of protein structure mentioned?
Denatured (unfolded) and native (folded).
p.53
Protein Misfolding and Associated Diseases
What does it mean when a protein is 50% unfolded?
It indicates that the protein is in a state of partial denaturation.
p.33
Methods for Protein Structural Determination
Why is the liquid method of structure determination in Biomolecular NMR considered more accurate?
Because it allows for the observation of proteins in a more native-like environment.
p.61
Favorable Interactions in Protein Folding
What happens during the formation of the hydrophobic core in proteins?
It releases ordered water molecules.
p.16
Secondary Structure: Alpha Helices and Beta Sheets
How do rapops interact in relation to β-sheets?
They interact less than in α-helices.
p.10
Protein Structure Overview
What bond angle is associated with trigonal planar geometry?
Approximately 120 degrees.
p.10
Protein Structure Overview
How does bond length vary with bond order?
As bond order increases, bond length decreases.
p.37
Fibrous vs. Globular Proteins
Where can α-Keratin be found?
In hair, feathers, and nails.
p.41
Protein Structure Overview
Do we need another enzyme to break down Vitamin C?
No, Vitamin C does not require another enzyme for breakdown.
p.51
Favorable Interactions in Protein Folding
What is the effect of reducing agents like DTT and BMG on proteins?
They reduce disulfide (S-S) bonds, affecting protein structure.
p.47
Protein Structure Overview
Why are motifs important in proteins?
Motifs are common in proteins with similar functions.
p.46
Protein Structure Overview
What type of structures do globular proteins have?
A variety of tertiary structures.
p.35
Methods for Protein Structural Determination
What does SDS PAGE stand for?
Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis.
p.26
Levels of Protein Structure: Primary to Quaternary
How many subunits does hemoglobin have?
It has 2 alpha and 2 beta subunits.
p.59
Protein Folding Thermodynamics
What are salt bridges in the context of protein folding?
Ionic interactions that stabilize the folded structure.
p.59
Protein Folding Thermodynamics
What type of interaction is London dispersion?
A weak intermolecular force that contributes to protein stability.
p.4
Favorable Interactions in Protein Folding
What interactions contribute to the stability of proteins?
Electrostatic interactions.
p.22
Levels of Protein Structure: Primary to Quaternary
What are the four levels of protein structure?
Primary, Secondary, Tertiary, and Quaternary.
p.62
Protein Folding Thermodynamics
What is the relationship between order and folding?
Folding increases order in the protein structure.
p.41
Protein Structure Overview
What are the requirements for the enzyme prolyl hydroxylase to function?
Oxygen (O2) and Vitamin C.
p.37
Fibrous vs. Globular Proteins
What are the characteristics of α-Keratin?
Tough, insoluble protective structures of varying hardness and flexibility.
p.18
Favorable Interactions in Protein Folding
What role does proline play in protein structure?
Proline can introduce kinks in polypeptide chains, affecting protein folding.
p.51
Favorable Interactions in Protein Folding
What role do hydrogen bonds play in protein stability?
Hydrogen bonding contributes to protein stability.
p.53
Protein Misfolding and Associated Diseases
What happens to proteins when they are denatured by heat?
They become inactive and lose their stability.
p.27
Methods for Protein Structural Determination
What is X-ray crystallography used for?
To determine protein structure.
p.49
Levels of Protein Structure: Primary to Quaternary
Can a given domain type be found in multiple proteins?
Yes, a given domain type may be found in several different proteins.
p.28
Methods for Protein Structural Determination
What limitation does X-ray crystallography have regarding hydrogen atoms?
It cannot resolve hydrogens.
p.35
Methods for Protein Structural Determination
What does the term 'diff' refer to in the context of SDS PAGE?
It likely refers to the difference in size between the subunits.
p.27
Methods for Protein Structural Determination
What is the third step in the X-ray crystallography process?
Collect X-ray diffraction data.
p.62
Protein Folding Thermodynamics
What does the term 'NET-TAS A' refer to in the context of protein folding?
It indicates the net thermodynamic stability associated with folding.
p.41
Protein Structure Overview
What is hydroxyproline's role in collagen?
It is a post-translational modification that enhances stability.
p.40
Levels of Protein Structure: Primary to Quaternary
How do collagen chains form a triple helix?
Three collagen chains intertwine into a right-handed superhelical triple helix stabilized with crosslinking.
p.2
Levels of Protein Structure: Primary to Quaternary
What are the main levels of protein structure?
Primary, secondary, tertiary, and quaternary.
p.2
Levels of Protein Structure: Primary to Quaternary
What determines the primary structure of a protein?
The sequence of amino acids in the polypeptide chain.
p.56
Anfinsen's Experiment and Protein Folding
What is reformed in Anfinsen's experiments?
The correct tertiary structure of RNase.
p.37
Fibrous vs. Globular Proteins
What are the characteristics of collagen?
High tensile strength, without stretch.
p.37
Fibrous vs. Globular Proteins
What are the characteristics of silk fibroin?
Soft, flexible filaments.
p.60
Fibrous vs. Globular Proteins
Where do hydrophobic residues typically point in globular proteins?
Inward, towards the core.
p.13
Secondary Structure: Alpha Helices and Beta Sheets
What is the issue with glycine in α-helices?
Glycine has a tiny R group, leading to too much rotation and instability.
p.56
Anfinsen's Experiment and Protein Folding
What is the native structure of proteins in terms of stability?
It is the thermodynamically most stable state.
p.51
Protein Misfolding and Associated Diseases
What effect does heat have on protein structure?
Heat can lead to denaturation of proteins.
