What happens to the charge of carboxyl and amino groups linked by a peptide bond?
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They carry no net charge.
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What happens to the charge of carboxyl and amino groups linked by a peptide bond?
They carry no net charge.
What is the charge of the N-terminus and C-terminus at neutral pH?
Both are charged.
What are proteins characterized by in terms of their structure?
Proteins have complicated conformations that impact their structure and function.
What does the primary structure of a protein refer to?
The sequence of amino acids in a protein.
How are the hydrogen bonds that stabilize the alpha-helix oriented?
They are nearly parallel to its central axis.
How are two glutathione molecules linked in the oxidized form?
Through a disulfide bond.
What does the term 'tripeptide' refer to?
A chain of three amino acids.
What does the quaternary structure of a protein involve?
The association of several completely folded polypeptide chains into a multisubunit or oligomeric protein.
What are examples of secondary structures in proteins?
Alpha helices, beta sheets, loops, and turns.
What direction do the side chains of amino acids in an alpha-helix point?
Outwards from the cylinder of the helix.
What is the reaction involving glutathione and reactive oxygen species?
2GSH + RO - OH → GSSG + H2O + ROH.
How many beta strands typically make up a beta sheet?
Between 2 to 15 strands.
What is the significance of the sequence VDLLKN in protein structure?
It can adopt different secondary structures depending on the protein context.
What type of bonds contribute to the stability and function of tertiary structure elements?
Covalent bonds, mainly disulfide bonds between 2 Cys residues.
What role do detergents like SDS play in protein denaturation?
They denature proteins by disrupting stabilizing hydrophobic interactions.
What is a polypeptide?
A chain of more than 20 amino acids.
What are the two forms of glutathione?
Reduced thiol form (GSH) and oxidized form (GSSG).
What stabilizes the helical conformation of alpha helices?
The cumulative effects of all the intrahelical hydrogen bonds.
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.
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.
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.
What primarily stabilizes tertiary structures?
Non-covalent bonds, most notably hydrophobic interactions.
What are lactate dehydrogenase and malate dehydrogenase examples of?
Homologous proteins with similar structure and function.
What are the free amino and carboxyl groups at the ends of a polypeptide chain called?
N-terminus and C-terminus, respectively.
What are examples of peptides with important physiological and biochemical functions?
Glutathione and endorphins.
What is generally involved in the separation of subunits in oligomeric proteins?
Breaking the strong hydrophobic interactions joining them together.
What is the 40 Helix - Loop - Helix motif?
A structural motif commonly found in proteins that facilitates binding to calcium ions.
What are the two structural elements distinguished in tertiary structures?
Motifs and Domains.
What stabilizes the native conformation of some proteins?
Disulfide bonds.
What is the significance of domains in proteins?
They are the smallest, terminally folded, functional elements of proteins.
What factors influence the Tm of proteins?
The pH and ionic strength of the solution.
What is the relative frequency of Glycine (Gly) in β sheet?
1.64
Which amino acid has the lowest relative frequency in α helix?
Proline (Pro) with 0.52.
What does the term 'b a b motifs' refer to?
A specific type of motif in protein structure.
What does the term 'dipeptide' refer to?
A chain of two amino acids.
How many potential conformations can a protein have?
A protein has an unlimited number of potential conformations.
Why can't the trans and cis conformations of a peptide bond be interconverted?
There is no rotation around the peptide bond.
What secondary structure does the sequence VDLLKN assume in one protein context?
α helix.
What is the orientation of hydrogen bonds in parallel β-sheets?
Hydrogen bonds are not perpendicular to the strands.
What happens to each subunit once separated from an oligomeric protein?
Each subunit maintains its native conformation.
What is the term for the disruption of the native conformation of a protein?
Denaturation.
What is the role of motifs in protein tertiary structure?
They are one of the structural elements based on their prevalence in protein conformations.
What generally happens to the function of denatured proteins?
They generally lose their function.
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.
Can the subunits in an oligomer be identical?
Yes, the subunits may be identical or different.
What is produced after denaturation of ribonuclease A?
A polypeptide chain containing 8 reduced sulfhydryl groups.
What structures do the disulfide bonds in ribonuclease A link?
Adjacent β-sheets, β-sheets to α-helices, or β-sheets to loops.
What occurs when urea is removed while maintaining a trace of 2-mercaptoethanol?
The protein refolds into its unique, active native structure.
What are linked amino acids in a polypeptide chain called?
Amino acid residues.
What are distinct elements of tertiary structure called?
Domains.
Can the secondary structure of proteins include variations?
Yes, it is not always repetitive.
What is glutathione primarily known for in mammalian cells?
It is a major antioxidant and sulfhydryl buffer.
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.
Why are Gly residues rare in alpha-helices?
Because the unrestricted rotation around their alpha-carbon destabilizes the helix.
How do amino acids arrange in alpha helices?
They wrap around an imaginary central axis in a right-handed screw motion.
What is the rise per residue in a right-handed alpha helix?
0.15 nm.
What type of proteins exhibit coiled coils, such as keratin?
Certain proteins.
How do hydrogen bonds form in parallel β-sheets?
Each residue forms hydrogen bonds with two different residues on the opposite strand.
Where can the beta strands in a beta sheet be located?
On separate polypeptides or on separate segments of the same polypeptide.
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).
What characterizes amphipathic alpha helices?
Hydrophobic amino acid side chains point in one direction, while hydrophilic side chains point in the opposite direction.
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.
What is the relative frequency of Alanine (Ala) in α helix?
1.29
How do the names of amino acid residues differ from free amino acids?
They are different to signal the difference.
What suffixes are replaced in the names of amino acid residues?
-ine, -ate, and -e are replaced by -yl.
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.
Why are Tyr and Asn residues less common in alpha-helices?
Because their bulky side chains cause significant hinderance.
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.
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.
What are beta strands?
Almost fully extended portions of the polypeptide chain.
What is the typical length range of an alpha helix?
From 4 or 5 residues to more than 40, with an average of 12.
What do characteristic folds in proteins form?
A common core with a specific structure and function.
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.
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.
What is the size range of domains?
From a few dozen to a few hundred amino acids.
What percentage of sequence identity do lactate dehydrogenase and malate dehydrogenase share?
23%.
Why is the modular structure of oligomeric proteins energetically favorable?
Different proteins can share the same subunits for similar functions.
What additional agents may be needed to disrupt potential disulfide bonds during denaturation?
Reducing agents.
What is required for the complete denaturation of ribonuclease A?
Reduction of disulfide bonds, disruption of hydrophobic interactions, and hydrogen bonds.
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.
Give examples of amino acid residues.
Glycil, glutamyl, glutaminyl, cysteinyl, asparaginyl, seryl, threonyl, and alanyl.
What is an oligopeptide?
A chain of less than 20 amino acids.
In which conformation do the two alpha-carbons lie on the same side of the peptide bond?
Cis conformation.
What is aspartame?
A modified simple peptide used as a food additive.
Which enzyme reduces oxidized glutathione?
Glutathione peroxidase.
What happens to the hydrophobic side of b-pleated sheets?
It packs into hydrophobic areas of proteins and membranes.
What secondary structure does the sequence VDLLKN assume in another protein context?
β strand.
What role do electrostatic forces play in oligomeric proteins?
They contribute to the association and may help in the proper alignment of the subunits.
How can domains be classified?
Based on the presence of characteristic folds, which are combinations of secondary structures and motifs.
How do proteins differ in relation to b-sheets?
Proteins differ in the amount of b-sheets their structure contains.
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.
What is an example of a motif that is associated with calcium binding proteins?
Helix-loop-helix.
How are the active sites of some oligomeric proteins formed?
From residues originating in different subunits.
What happens to the 3-D structure of oligomeric proteins upon substrate binding?
It changes, affecting both tertiary and quaternary structure.
What characterizes the b-category of protein domains?
Domains made almost entirely of b-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.
How many possible pairings exist for the 8 sulfhydryl groups?
105 possible pairings.
In what direction are amino acid residues in a polypeptide numbered?
From the N-terminus to the C-terminus.
What are the two conformations of a peptide bond?
Trans and cis.
Why are Ala residues common in alpha-helices?
Because the small side chain does not disrupt the helical structure.
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.
What is the other common secondary structure besides alpha helices?
Beta structure.
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).
What structures are formed by multiple beta strands arranged side by side?
Beta sheets.
Who first studied the renaturation pathway of ribonuclease A?
Afinsen and colleagues.
What is the length of the ribonuclease A protein?
124 amino acids.
What are homologous proteins?
Proteins that have similar functions and structures, despite limited sequence similarity.
How are protein domains classified?
By their dominant secondary structure.
What characterizes the a-category of protein domains?
Domains made primarily of a-helices.
Can small denatured proteins spontaneously renature or refold?
Yes, but it is rare.
What is the relative frequency of Aspartic acid (Asp) in turn?
1.41
Which reagents can achieve the reduction of disulfide bonds in ribonuclease A?
2-mercaptoethanol or other thiol reagents.
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.
What is the stable conformation of a protein under physiological conditions called?
The native conformation.
Why are nearly all peptide groups in a protein in the trans conformation?
Due to steric hindrance between side chains.
What is the typical concentration of glutathione in mammalian cells?
5 mM.
What type of damage does glutathione protect cells from?
Damage caused by reactive oxygen species such as hydrogen peroxide and organic peroxides.
What are the components of secondary structures in proteins?
Alpha helices, beta-pleated strands (beta sheets), loops, and turns.
What is the pitch of a right-handed alpha helix?
0.54 nm.
How many amino acid residues are there in one complete turn of an alpha helix?
3.6 amino acid residues.
What is the orientation of hydrogen bonds in antiparallel β-sheets?
Hydrogen bonds are perpendicular to the strands that form them.
What orientation do hydrophilic sides of helices have when on the surface of proteins?
The hydrophilic side points outwards.
Why are parallel sheets less stable than antiparallel sheets?
Possibly because of the angles of the hydrogen bonds holding the strands.
How do water molecules affect protein conformation?
They disrupt hydrophobic interactions that stabilize the native conformation of the protein.
What are the compact structural units in the tertiary structure of certain proteins called?
Domains.
What do domains consist of?
Several motifs and independent secondary structure elements.
What is a characteristic of oligomeric proteins regarding stability?
Oligomers are usually more stable than their individual subunits.
Which amino acid has the highest relative frequency in β sheet?
Valine (Val) with 1.49.
How are domains generally connected in a protein?
By loops.
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.
How many disulfide bonds does ribonuclease A have?
4 disulfide bonds.
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.
In which conformation are the two alpha-carbons on opposite sides of the peptide bond?
Trans conformation.
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.
What are some examples of potent toxins derived from peptides?
Snake venom, mushroom toxins, and bacterial toxins.
What do subunits of oligomeric proteins do?
They remain stably associated and behave as a single unit with one or several functions.
What is the average content of alpha helices in a protein?
Approximately 26%.
How do the amino acid side chains of b-sheets orient?
They point alternatively above and below the plane of the sheet.
How much energy is needed to denature proteins?
Relatively small, as low as the energy needed to disrupt one to two dozen hydrogen bonds.
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.
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.
Which motif is commonly found in DNA binding proteins?
Helix-turn-helix.
What is a characteristic feature of helix bundles?
They are a type of motif in protein structure.
What is required for the formation of disulfide bonds?
The oxidation of thiol groups of Cys residues by disulfide exchange reactions involving oxidized glutathione.
What similarities does cytochrome c have across different species?
Similar structure, function, and comparable sequence.
What is the relative frequency of Serine (Ser) in β sheet?
0.95
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.
What contributes most of the ionic charges associated with a protein?
The side chains of its amino acid residues.
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.
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.
What is the concentration of urea in the solution?
62.8 M.
How do beta sheets typically appear in the final conformation of most proteins?
They are mostly twisted, distorted, and buckled.
What are b-sheets also called?
b-pleated sheets.
What role does Calmodulin play in cellular processes?
Calmodulin acts as a calcium sensor and mediates various cellular responses to calcium levels.
What residues are involved in the formation of disulfide bonds?
Cysteine (Cys) residues.
What is the characteristic 'melting' temperature Tm of proteins?
The temperature at the mid-point between the native and denatured forms.
What is a multi-subunit protein called?
Oligomer.
What is each subunit in an oligomer?
A separate polypeptide chain in its final conformation.
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.
What is the relative frequency of Cysteine (Cys) in turn?
0.80
What does denaturation indicate about the temperature range?
It takes place over a narrow range of temperatures.
What is the relative frequency of Phenylalanine (Phe) in α helix?
1.07
What structural feature can b-pleated sheets exhibit?
Amphipathicity, with hydrophilic residues on one side and hydrophobic residues on the opposite side.
What type of bonds usually hold the subunits of oligomeric proteins together?
Non-covalent bonds, most notably hydrophobic interactions.
What kind of twist do beta sheets present as they progress?
A slight right-handed twist.
What is tertiary structure in proteins?
The folding of several secondary structure elements into a closely-packed, 3-D, completely folded, functional protein.
What is an example of a helical motif where certain amino acids are located on one side?
Leucine zippers in DNA binding motifs.
What is quaternary structure in proteins?
An additional level of structural complexity where different protein subunits associate to form a fully functional protein.
What happens to ribonuclease A when in conditions that favor its stable native conformation?
It refolds quickly.
What do homologous proteins demonstrate?
The same structure and function.
What does the renaturation of ribonuclease A demonstrate about proteins?
That proteins can refold spontaneously.
What happens if the subunits of an oligomer are different?
The oligomer will have different functions.
What is a b-sandwich motif?
A type of motif in protein structure.
What is required to completely denature a protein?
An input of energy.
What is the role of domains in protein tertiary structure?
They are one of the structural elements based on their prevalence in protein conformations.
What agents can denature proteins?
Chaotropic agents and detergents.
What determines the position of domains in the final fold of a protein?
Non-covalent interactions with other domains and structural elements.
What is a major regulatory factor of protein activity in oligomeric proteins?
The change in structure upon substrate binding.
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.
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.
What are coiled coil motifs?
A type of motif in protein structure.
Which homologous protein is conserved among species?
Cytochrome c.
Which amino acid has a relative frequency of 1.00 in turn?
Glutamic acid (Glu).
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.
What is the primary focus of BCH300 Lecture 4?
Proteins.
What are proteins made of?
Polymers of amino acids joined together by peptide bonds.
