p.2
Amino Acids and Peptide Bonds
What are proteins made of?
Polymers of amino acids joined together by peptide bonds.
p.2
Amino Acids and Peptide Bonds
What happens to the charge of carboxyl and amino groups linked by a peptide bond?
They carry no net charge.
p.8
Protein Conformation and Stability
What are proteins characterized by in terms of their structure?
Proteins have complicated conformations that impact their structure and function.
p.9
Levels of Protein Structure
What does the primary structure of a protein refer to?
The sequence of amino acids in a protein.
p.18
Secondary Structure: Alpha Helices and Beta Sheets
How are the hydrogen bonds that stabilize the alpha-helix oriented?
They are nearly parallel to its central axis.
p.6
Amino Acids and Peptide Bonds
How are two glutathione molecules linked in the oxidized form?
Through a disulfide bond.
p.4
Polypeptide Chains and Terminology
What does the term 'tripeptide' refer to?
A chain of three amino acids.
p.10
Quaternary Structure and Oligomeric Proteins
What does the quaternary structure of a protein involve?
The association of several completely folded polypeptide chains into a multisubunit or oligomeric protein.
p.9
Secondary Structure: Alpha Helices and Beta Sheets
What are examples of secondary structures in proteins?
Alpha helices, beta sheets, loops, and turns.
p.19
Secondary Structure: Alpha Helices and Beta Sheets
What direction do the side chains of amino acids in an alpha-helix point?
Outwards from the cylinder of the helix.
p.6
Physiological Functions of Peptides
What is the reaction involving glutathione and reactive oxygen species?
2GSH + RO - OH → GSSG + H2O + ROH.
p.34
Secondary Structure: Alpha Helices and Beta Sheets
What is the significance of the sequence VDLLKN in protein structure?
It can adopt different secondary structures depending on the protein context.
p.37
Tertiary Structure and Protein Folding
What type of bonds contribute to the stability and function of tertiary structure elements?
Covalent bonds, mainly disulfide bonds between 2 Cys residues.
p.57
Denaturation and Renaturation of Proteins
What role do detergents like SDS play in protein denaturation?
They denature proteins by disrupting stabilizing hydrophobic interactions.
p.4
Polypeptide Chains and Terminology
What is a polypeptide?
A chain of more than 20 amino acids.
p.6
Amino Acids and Peptide Bonds
What are the two forms of glutathione?
Reduced thiol form (GSH) and oxidized form (GSSG).
p.20
Secondary Structure: Alpha Helices and Beta Sheets
What stabilizes the helical conformation of alpha helices?
The cumulative effects of all the intrahelical hydrogen bonds.
p.27
Secondary Structure: Alpha Helices and Beta Sheets
How do hydrogen bonds form in antiparallel β-sheets?
The carbonyl oxygen and the amide nitrogen of each residue form hydrogen bonds with a single residue on the opposite chain.
p.23
Protein Conformation and Stability
How do hydrophobic residues interact in coiled coils of keratin?
Hydrophobic residues on one side of the helix interact with those of the other helix to form the coil.
p.36
Tertiary Structure and Protein Folding
What does tertiary structure do to residues in a protein?
It brings together residues that are far apart in the primary sequence into functional units, such as enzyme active sites.
p.36
Tertiary Structure and Protein Folding
What primarily stabilizes tertiary structures?
Non-covalent bonds, most notably hydrophobic interactions.
p.46
Structure and Function of Proteins
What are lactate dehydrogenase and malate dehydrogenase examples of?
Homologous proteins with similar structure and function.
p.4
Polypeptide Chains and Terminology
What are the free amino and carboxyl groups at the ends of a polypeptide chain called?
N-terminus and C-terminus, respectively.
p.5
Physiological Functions of Peptides
What are examples of peptides with important physiological and biochemical functions?
Glutathione and endorphins.
p.52
Quaternary Structure and Oligomeric Proteins
What is generally involved in the separation of subunits in oligomeric proteins?
Breaking the strong hydrophobic interactions joining them together.
p.40
Protein Conformation and Stability
What is the 40 Helix - Loop - Helix motif?
A structural motif commonly found in proteins that facilitates binding to calcium ions.
p.41
Tertiary Structure and Protein Folding
What is the significance of domains in proteins?
They are the smallest, terminally folded, functional elements of proteins.
p.56
Denaturation and Renaturation of Proteins
What factors influence the Tm of proteins?
The pH and ionic strength of the solution.
p.38
Levels of Protein Structure
What does the term 'b a b motifs' refer to?
A specific type of motif in protein structure.
p.4
Polypeptide Chains and Terminology
What does the term 'dipeptide' refer to?
A chain of two amino acids.
p.8
Protein Conformation and Stability
How many potential conformations can a protein have?
A protein has an unlimited number of potential conformations.
p.11
Peptide Bonds and Terminology
Why can't the trans and cis conformations of a peptide bond be interconverted?
There is no rotation around the peptide bond.
p.27
Secondary Structure: Alpha Helices and Beta Sheets
What is the orientation of hydrogen bonds in parallel β-sheets?
Hydrogen bonds are not perpendicular to the strands.
p.52
Quaternary Structure and Oligomeric Proteins
What happens to each subunit once separated from an oligomeric protein?
Each subunit maintains its native conformation.
p.37
Tertiary Structure and Protein Folding
What is the role of motifs in protein tertiary structure?
They are one of the structural elements based on their prevalence in protein conformations.
p.54
Denaturation and Renaturation of Proteins
What generally happens to the function of denatured proteins?
They generally lose their function.
p.60
Tertiary Structure and Protein Folding
What significant implication did Afinsen's work have regarding protein structure?
It implied that the tertiary structure of a protein is dictated by its sequence.
p.49
Quaternary Structure and Oligomeric Proteins
Can the subunits in an oligomer be identical?
Yes, the subunits may be identical or different.
p.61
Denaturation and Renaturation of Proteins
What is produced after denaturation of ribonuclease A?
A polypeptide chain containing 8 reduced sulfhydryl groups.
p.58
Levels of Protein Structure
What structures do the disulfide bonds in ribonuclease A link?
Adjacent β-sheets, β-sheets to α-helices, or β-sheets to loops.
p.61
Denaturation and Renaturation of Proteins
What occurs when urea is removed while maintaining a trace of 2-mercaptoethanol?
The protein refolds into its unique, active native structure.
p.9
Levels of Protein Structure
Can the secondary structure of proteins include variations?
Yes, it is not always repetitive.
p.6
Physiological Functions of Peptides
What is glutathione primarily known for in mammalian cells?
It is a major antioxidant and sulfhydryl buffer.
p.19
Secondary Structure: Alpha Helices and Beta Sheets
How do the side chains of amino acids affect the stability of the alpha-helix?
The identity of these side chains affects the stability of the helix.
p.19
Secondary Structure: Alpha Helices and Beta Sheets
Why are Gly residues rare in alpha-helices?
Because the unrestricted rotation around their alpha-carbon destabilizes the helix.
p.15
Secondary Structure: Alpha Helices and Beta Sheets
How do amino acids arrange in alpha helices?
They wrap around an imaginary central axis in a right-handed screw motion.
p.27
Secondary Structure: Alpha Helices and Beta Sheets
How do hydrogen bonds form in parallel β-sheets?
Each residue forms hydrogen bonds with two different residues on the opposite strand.
p.26
Secondary Structure: Alpha Helices and Beta Sheets
Where can the beta strands in a beta sheet be located?
On separate polypeptides or on separate segments of the same polypeptide.
p.24
Secondary Structure: Alpha Helices and Beta Sheets
How do beta strands compare in compactness to helices?
Beta strands are significantly less compact (0.32 nm/residue vs 0.15 nm/residue for helices).
p.22
Secondary Structure: Alpha Helices and Beta Sheets
What characterizes amphipathic alpha helices?
Hydrophobic amino acid side chains point in one direction, while hydrophilic side chains point in the opposite direction.
p.40
Tertiary Structure and Protein Folding
How does the 40 Helix - Loop - Helix motif contribute to Calmodulin's function?
It allows Calmodulin to undergo conformational changes upon calcium binding, enabling it to interact with target proteins.
p.3
Polypeptide Chains and Terminology
How do the names of amino acid residues differ from free amino acids?
They are different to signal the difference.
p.3
Polypeptide Chains and Terminology
What suffixes are replaced in the names of amino acid residues?
-ine, -ate, and -e are replaced by -yl.
p.8
Protein Conformation and Stability
What is a conformation in the context of proteins?
A conformation is a spatial arrangement of atoms that depends on the rotation of different covalent bonds.
p.19
Secondary Structure: Alpha Helices and Beta Sheets
Why are Tyr and Asn residues less common in alpha-helices?
Because their bulky side chains cause significant hinderance.
p.20
Secondary Structure: Alpha Helices and Beta Sheets
What are the dipole characteristics of alpha helices?
They have a positive N-terminus and a negative C-terminus, with each peptide bond being polar and all hydrogen bonds pointing in the same direction.
p.32
Secondary Structure: Alpha Helices and Beta Sheets
What is the relationship between the hydrophilic side of b-pleated sheets and the aqueous environment?
The hydrophilic side remains in contact with the aqueous milieu.
p.24
Secondary Structure: Alpha Helices and Beta Sheets
What are beta strands?
Almost fully extended portions of the polypeptide chain.
p.22
Secondary Structure: Alpha Helices and Beta Sheets
What is the typical length range of an alpha helix?
From 4 or 5 residues to more than 40, with an average of 12.
p.45
Levels of Protein Structure
What do characteristic folds in proteins form?
A common core with a specific structure and function.
p.38
Levels of Protein Structure
What are motifs in protein structure?
Recognizable combinations of helices, sheets, and loops that appear in different proteins and generally have the same conserved function.
p.57
Protein Conformation and Stability
When do disulfide bonds occur in proteins?
When the side chains of two Cys residues lie within close proximity in the final conformation of the protein.
p.41
Tertiary Structure and Protein Folding
What is the size range of domains?
From a few dozen to a few hundred amino acids.
p.53
Quaternary Structure and Oligomeric Proteins
Why is the modular structure of oligomeric proteins energetically favorable?
Different proteins can share the same subunits for similar functions.
p.58
Denaturation and Renaturation of Proteins
What is required for the complete denaturation of ribonuclease A?
Reduction of disulfide bonds, disruption of hydrophobic interactions, and hydrogen bonds.
p.2
Peptide Bonds and Terminology
How are peptide bonds formed?
Through the condensation of the α-carboxyl group of one amino acid with the α-amino group of another, resulting in a dipeptide and the loss of one water molecule.
p.3
Polypeptide Chains and Terminology
Give examples of amino acid residues.
Glycil, glutamyl, glutaminyl, cysteinyl, asparaginyl, seryl, threonyl, and alanyl.
p.4
Polypeptide Chains and Terminology
What is an oligopeptide?
A chain of less than 20 amino acids.
p.5
Physiological Functions of Peptides
What is aspartame?
A modified simple peptide used as a food additive.
p.32
Secondary Structure: Alpha Helices and Beta Sheets
What happens to the hydrophobic side of b-pleated sheets?
It packs into hydrophobic areas of proteins and membranes.
p.50
Quaternary Structure and Oligomeric Proteins
What role do electrostatic forces play in oligomeric proteins?
They contribute to the association and may help in the proper alignment of the subunits.
p.45
Levels of Protein Structure
How can domains be classified?
Based on the presence of characteristic folds, which are combinations of secondary structures and motifs.
p.29
Secondary Structure: Alpha Helices and Beta Sheets
How do proteins differ in relation to b-sheets?
Proteins differ in the amount of b-sheets their structure contains.
p.45
Levels of Protein Structure
What is the relationship between common motifs, folds, and domains in proteins?
They exist in a variety of proteins and indicate similar functions and structures.
p.53
Quaternary Structure and Oligomeric Proteins
How are the active sites of some oligomeric proteins formed?
From residues originating in different subunits.
p.53
Quaternary Structure and Oligomeric Proteins
What happens to the 3-D structure of oligomeric proteins upon substrate binding?
It changes, affecting both tertiary and quaternary structure.
p.44
Secondary Structure: Alpha Helices and Beta Sheets
What characterizes the b-category of protein domains?
Domains made almost entirely of b-sheets.
p.44
Secondary Structure: Alpha Helices and Beta Sheets
What defines the a/b category of protein domains?
Domains made of b-a-b motifs and other structures where helix and sheet regions alternate.
p.4
Polypeptide Chains and Terminology
In what direction are amino acid residues in a polypeptide numbered?
From the N-terminus to the C-terminus.
p.19
Secondary Structure: Alpha Helices and Beta Sheets
Why are Ala residues common in alpha-helices?
Because the small side chain does not disrupt the helical structure.
p.26
Secondary Structure: Alpha Helices and Beta Sheets
What are the stable structures that proteins contain instead of individual beta strands?
Beta sheets, which are highly stable structures held together by hydrogen bonds.
p.26
Secondary Structure: Alpha Helices and Beta Sheets
What are the two types of beta strands that can form a beta sheet?
Parallel beta strands (same N to C-terminal direction) and antiparallel strands (opposite N to C-terminal direction).
p.45
Levels of Protein Structure
What are homologous proteins?
Proteins that have similar functions and structures, despite limited sequence similarity.
p.44
Levels of Protein Structure
How are protein domains classified?
By their dominant secondary structure.
p.44
Secondary Structure: Alpha Helices and Beta Sheets
What characterizes the a-category of protein domains?
Domains made primarily of a-helices.
p.58
Denaturation and Renaturation of Proteins
Which reagents can achieve the reduction of disulfide bonds in ribonuclease A?
2-mercaptoethanol or other thiol reagents.
p.10
Tertiary Structure and Protein Folding
What does the tertiary structure of a protein refer to?
The assembly of different secondary structural motifs into a well-organized final conformation of the completely folded protein.
p.11
Peptide Bonds and Terminology
Why are nearly all peptide groups in a protein in the trans conformation?
Due to steric hindrance between side chains.
p.6
Physiological Functions of Peptides
What type of damage does glutathione protect cells from?
Damage caused by reactive oxygen species such as hydrogen peroxide and organic peroxides.
p.15
Secondary Structure: Alpha Helices and Beta Sheets
What are the components of secondary structures in proteins?
Alpha helices, beta-pleated strands (beta sheets), loops, and turns.
p.27
Secondary Structure: Alpha Helices and Beta Sheets
What is the orientation of hydrogen bonds in antiparallel β-sheets?
Hydrogen bonds are perpendicular to the strands that form them.
p.23
Protein Conformation and Stability
What orientation do hydrophilic sides of helices have when on the surface of proteins?
The hydrophilic side points outwards.
p.29
Secondary Structure: Alpha Helices and Beta Sheets
Why are parallel sheets less stable than antiparallel sheets?
Possibly because of the angles of the hydrogen bonds holding the strands.
p.57
Denaturation and Renaturation of Proteins
How do water molecules affect protein conformation?
They disrupt hydrophobic interactions that stabilize the native conformation of the protein.
p.41
Tertiary Structure and Protein Folding
What do domains consist of?
Several motifs and independent secondary structure elements.
p.53
Quaternary Structure and Oligomeric Proteins
What is a characteristic of oligomeric proteins regarding stability?
Oligomers are usually more stable than their individual subunits.
p.46
Structure and Function of Proteins
What can some proteins have in terms of homologous domains?
One or two homologous domains with the same function while the rest of the protein has a different structure.
p.55
Denaturation and Renaturation of Proteins
What does it mean that protein unfolding is a cooperative process?
A few weak interactions destabilized can lead to the complete loss of native conformation.
p.18
Secondary Structure: Alpha Helices and Beta Sheets
What is the hydrogen bonding pattern within an alpha-helix?
Each carbonyl oxygen (residue n) is hydrogen bonded to the backbone amide hydrogen of residue n + 4.
p.5
Physiological Functions of Peptides
What are some examples of potent toxins derived from peptides?
Snake venom, mushroom toxins, and bacterial toxins.
p.52
Quaternary Structure and Oligomeric Proteins
What do subunits of oligomeric proteins do?
They remain stably associated and behave as a single unit with one or several functions.
p.29
Secondary Structure: Alpha Helices and Beta Sheets
How do the amino acid side chains of b-sheets orient?
They point alternatively above and below the plane of the sheet.
p.54
Denaturation and Renaturation of Proteins
How much energy is needed to denature proteins?
Relatively small, as low as the energy needed to disrupt one to two dozen hydrogen bonds.
p.54
Denaturation and Renaturation of Proteins
What can happen to proteins depending on the amount of energy used during denaturation?
They can become entirely denatured to form random coils or retain certain structural elements while losing others.
p.44
Levels of Protein Structure
What are domain structures in proteins?
They are structural units that can be common to different proteins or unique to specific proteins with particular structure/function.
p.38
Levels of Protein Structure
What is a characteristic feature of helix bundles?
They are a type of motif in protein structure.
p.58
Amino Acids and Peptide Bonds
What is required for the formation of disulfide bonds?
The oxidation of thiol groups of Cys residues by disulfide exchange reactions involving oxidized glutathione.
p.46
Structure and Function of Proteins
What similarities does cytochrome c have across different species?
Similar structure, function, and comparable sequence.
p.9
Levels of Protein Structure
What is the secondary structure of a protein?
Regular, repetitive structural motifs that bring the primary structure into the first level of 3D conformational organization.
p.5
Amino Acids and Peptide Bonds
What contributes most of the ionic charges associated with a protein?
The side chains of its amino acid residues.
p.20
Secondary Structure: Alpha Helices and Beta Sheets
Why are proline residues rare in alpha helices?
Because their rigid cyclic side chains disrupt the helix and they cannot participate in intrahelical hydrogen bonding.
p.20
Secondary Structure: Alpha Helices and Beta Sheets
Where do the hydrogen bonds in alpha helices occur, and why are they stable?
In the hydrophobic interior of the helix, where few water molecules enter, making them particularly stable.
p.31
Secondary Structure: Alpha Helices and Beta Sheets
How do beta sheets typically appear in the final conformation of most proteins?
They are mostly twisted, distorted, and buckled.
p.40
Physiological Functions of Peptides
What role does Calmodulin play in cellular processes?
Calmodulin acts as a calcium sensor and mediates various cellular responses to calcium levels.
p.56
Denaturation and Renaturation of Proteins
What is the characteristic 'melting' temperature Tm of proteins?
The temperature at the mid-point between the native and denatured forms.
p.49
Quaternary Structure and Oligomeric Proteins
What is each subunit in an oligomer?
A separate polypeptide chain in its final conformation.
p.56
Denaturation and Renaturation of Proteins
How do high concentrations of chaotropic agents like Urea and Guanidinium salts denature proteins?
By allowing water molecules to solvate non-polar groups in the interior of proteins.
p.55
Denaturation and Renaturation of Proteins
What does denaturation indicate about the temperature range?
It takes place over a narrow range of temperatures.
p.32
Secondary Structure: Alpha Helices and Beta Sheets
What structural feature can b-pleated sheets exhibit?
Amphipathicity, with hydrophilic residues on one side and hydrophobic residues on the opposite side.
p.50
Quaternary Structure and Oligomeric Proteins
What type of bonds usually hold the subunits of oligomeric proteins together?
Non-covalent bonds, most notably hydrophobic interactions.
p.31
Secondary Structure: Alpha Helices and Beta Sheets
What kind of twist do beta sheets present as they progress?
A slight right-handed twist.
p.36
Tertiary Structure and Protein Folding
What is tertiary structure in proteins?
The folding of several secondary structure elements into a closely-packed, 3-D, completely folded, functional protein.
p.22
Secondary Structure: Alpha Helices and Beta Sheets
What is an example of a helical motif where certain amino acids are located on one side?
Leucine zippers in DNA binding motifs.
p.49
Quaternary Structure and Oligomeric Proteins
What is quaternary structure in proteins?
An additional level of structural complexity where different protein subunits associate to form a fully functional protein.
p.45
Levels of Protein Structure
What do homologous proteins demonstrate?
The same structure and function.
p.60
Protein Conformation and Stability
What does the renaturation of ribonuclease A demonstrate about proteins?
That proteins can refold spontaneously.
p.49
Quaternary Structure and Oligomeric Proteins
What happens if the subunits of an oligomer are different?
The oligomer will have different functions.
p.38
Levels of Protein Structure
What is a b-sandwich motif?
A type of motif in protein structure.
p.37
Tertiary Structure and Protein Folding
What is the role of domains in protein tertiary structure?
They are one of the structural elements based on their prevalence in protein conformations.
p.56
Denaturation and Renaturation of Proteins
What agents can denature proteins?
Chaotropic agents and detergents.
p.41
Tertiary Structure and Protein Folding
What determines the position of domains in the final fold of a protein?
Non-covalent interactions with other domains and structural elements.
p.53
Quaternary Structure and Oligomeric Proteins
What is a major regulatory factor of protein activity in oligomeric proteins?
The change in structure upon substrate binding.
p.44
Secondary Structure: Alpha Helices and Beta Sheets
What is the a+b category of protein domains?
Domains that consist of local clusters of a-helices and b-sheets that are separate and do not alternate.
p.61
Denaturation and Renaturation of Proteins
What is the effect of denaturation of ribonuclease A using 8 M urea and 2-mercaptoethanol?
It results in complete loss of tertiary structure and activity.
p.38
Levels of Protein Structure
What are coiled coil motifs?
A type of motif in protein structure.
p.61
Denaturation and Renaturation of Proteins
What happens when 2-mercaptoethanol is removed and oxidation occurs in the presence of urea?
The sulfhydryl groups pair randomly, resulting in an incorrectly folded protein.
