Protein Structure and α Helices Quiz

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Questions and Answers

What feature of the α helix contributes to its stability?

Side chains are buried within the helix

Maximum number of hydrogen bonds (correct)

A minimal number of hydrogen bonds

Irregular arrangement of side chains

Which of the following describes the arrangement of the backbone atoms in a segment with regular secondary structure?

Fluctuating φ and ψ values throughout the segment

Irregular backbone arrangement

Random arrangement of φ and ψ values

Constant φ and ψ values throughout the segment (correct)

What is the typical number of residues in one turn of an α helix?

5 residues

3.6 residues (correct)

4 residues

3 residues

Which of these statements about the inner diameter of the α helix is true?

It is approximately 4–5 Å Signup and view all the answers

What type of sequence is likely to produce an α helix with a hydrophobic face?

A sequence predominantly composed of hydrophobic residues Signup and view all the answers

Which of the following statements is true regarding the stability of protein structures?

Noncovalent interactions are the most important forces stabilizing protein structure. Signup and view all the answers

What aspect of protein structure is primarily determined by the amino acid sequence?

The three-dimensional structure of the protein. Signup and view all the answers

Which of the following correctly describes a characteristic of natural protein structures?

They usually exist in one or few stable structures. Signup and view all the answers

Which force is NOT typically associated with stabilizing protein structures?

Covalent interactions Signup and view all the answers

What dictates the specific functions of proteins in relation to their three-dimensional structure?

The uniqueness of their three-dimensional structures. Signup and view all the answers

What is the role of a modulator in allosteric proteins?

To induce a conformational change in the protein Signup and view all the answers

Which of the following statements about homotropic and heterotropic modulators is correct?

Homotropic modulators increase binding affinity Signup and view all the answers

What effect does carbon monoxide (CO) have on hemoglobin?

It occupies binding sites more effectively than oxygen Signup and view all the answers

What information can be gathered from the Hill coefficient (nH)?

An nH value of 1 indicates non-cooperative binding Signup and view all the answers

In which scenario would you expect an increase in the value of Y using the given expressions?

Increasing the affinity of the ligand for the protein Signup and view all the answers

What does the term 'cooperative binding' imply regarding ligand attachment to a protein?

The binding of one ligand increases the affinity for additional ligand binding Signup and view all the answers

What condition is indicated by a Hill coefficient greater than 1?

The protein exhibits positive cooperativity Signup and view all the answers

If a newly discovered protein has multiple subunits, what can be inferred about its ligand-binding capacity?

It may exhibit cooperative binding behavior Signup and view all the answers

What role do amino acid R chain interactions play in the stability of the α helix?

They can either stabilize or destabilize the α helix. Signup and view all the answers

What is the effect of proline on an α helix?

Proline introduces a destabilizing kink in the helix. Signup and view all the answers

What defines binding energy in the context of enzyme activity?

The energy derived from noncovalent enzyme-substrate interaction Signup and view all the answers

Which amino acid is often found near the NH3+ terminus of an α helix?

Negatively charged amino acids Signup and view all the answers

Which of the following is NOT a factor included in the barrier to reaction, ∆G‡?

The concentration of enzyme molecules Signup and view all the answers

How does binding energy influence substrate interaction during enzymatic reactions?

It constrains substrates into the proper orientation to react Signup and view all the answers

How are adjacent polypeptide chains oriented in a β sheet?

They can be either antiparallel or parallel. Signup and view all the answers

What is a defining characteristic of β turns in proteins?

They always involve Gly and Pro at specific positions. Signup and view all the answers

What is desolvation in the context of enzyme-substrate interaction?

The removal of structured water around the substrate Signup and view all the answers

What primarily provides the energy for enzymes to lower activation energies?

Noncovalent enzyme-substrate interaction Signup and view all the answers

What does the tertiary structure of a protein describe?

The overall three-dimensional arrangement of all atoms. Signup and view all the answers

Which aspect is crucial for enzyme specificity?

Ability to discriminate against a competing molecule Signup and view all the answers

What characterizes the quaternary structure of a protein?

It encompasses multiple polypeptide chains in a complex. Signup and view all the answers

Which of the following statements about β strands is correct?

They are single segments that contribute to the overall β conformation. Signup and view all the answers

What role does entropy reduction play in enzymatic reactions?

It restricts the movements of substrates to increase interaction Signup and view all the answers

What is the result of optimized binding energy in the transition state?

Improved substrate positioning in the active site Signup and view all the answers

What occurs during the pre-steady state of enzyme-substrate interaction?

[ES] increases until it reaches a constant level. Signup and view all the answers

What characterizes the saturation effect in enzyme kinetics?

There is a constant linear increase in the reaction rate with substrate concentration. Signup and view all the answers

Which step in the Michaelis-Menten model occurs first?

Enzyme and substrate combine to form the ES complex. Signup and view all the answers

Why does Vmax occur in enzyme kinetics?

The enzyme is fully saturated with substrate, forming ES complexes. Signup and view all the answers

What does a decrease in [S] during the pre-steady state indicate?

The substrate is being converted to product. Signup and view all the answers

Which statement correctly describes the relationship between substrate concentration and reaction rate at Vmax?

The reaction rate reaches a maximum and does not increase further. Signup and view all the answers

In the context of enzyme kinetics, what does the term 'pre-steady state' refer to?

The initial phase when the ES complex concentration stabilizes. Signup and view all the answers

Which of the following best describes the role of ES complex in enzyme kinetics?

It is essential for the rate-limiting step in the reaction. Signup and view all the answers

Study Notes

Biochemistry Study Notes

Biochemistry is the chemistry of living matter.
The basis of all life is the chemical reactions that take place within the cell.
Living organisms have a high degree of complexity and organization.
They extract, transform, and systematically use energy to create and maintain structures and perform work.
The interactions of individual components are dynamic and coordinated.
Living organisms have the ability to sense and respond to changes in their surroundings
They have a capacity for fairly precise self-replication while allowing enough change for evolution.
Biological processes can be studied in vivo (in the living), in vitro (in glass, test tubes), or in silico (computer simulations).
The environment within cells differs significantly from the environment in a test tube.
The cytosol is crowded, reducing diffusion of molecules and increasing friction.

Essential Elements for Life

Other than carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur are also common elements in living organisms.
Metal ions (e.g., potassium, sodium, calcium, magnesium, zinc, iron) play important roles in metabolism.
The human body is predominantly composed of oxygen (65%), carbon (18%), hydrogen (10%), and nitrogen (3%).
Earth's crust is mainly composed of oxygen (49%), silicon (26%), aluminum (8%), iron(5%).

The Carbon Atom

Carbon's ability to form very stable bonds with up to four other atoms (including other carbon atoms) is crucial for the formation of complex molecules.
Single carbon-carbon bonds have a length of 0.154 nm, and double bonds have a length of 0.134 nm.

Functional Groups of Biological Molecules

Functional groups influence the properties of biological molecules.
Examples include methyl, ethyl, phenyl, carbonyl, carboxyl, ester, ether, amino, imidazole, hydroxyle, enol, guanidinium, etc.
Functional groups are present in diverse biological molecules like proteins, sugars, nucleic acids.

Stereoisomers

Stereoisomers have different physical properties.
They have the same chemical bonds but different configurations around the bonds.
Stereoisomers cannot be interconverted without temporarily breaking one or more covalent bonds.
Configuration arises due to double bonds and chiral centers.

Water: The Medium of Life

Organisms typically contain 70-90% water.
Chemical reactions occur in an aqueous solution.
Water's structure and properties heavily influence protein, nucleic acid, and membrane function.

Hydrogen Bonds

Hydrogen bonds are strong dipole-dipole interactions arising between a covalently bound hydrogen and a lone electron pair on another electronegative atom (often nitrogen or oxygen).
Hydrogen bonds are strongest when molecules allow for linear bonding patterns, ideally with the three atoms involved in a straight line.

Hydrogen Bonding in Water

Water can serve as both a hydrogen bond donor and acceptor.
Up to four hydrogen bonds per water molecule are possible.
This leads to high boiling and melting points, large surface tension, and cooperative interactions.
The strength of hydrogen bonds in water is weak relative to the covalent strength of the H-O bonds in water molecules

Noncovalent and Van Der Waals Interactions

Weak interactions between atoms, regardless of polarity.
Attractive (London dispersion) and repulsive (steric) components
The attractive force dominates at longer distances (typically 0.4–0.7 nm).
Repulsion dominates at extremely short distances.
Interactions have a minimum energy distance (van der Waals radius)
Van der Waals radii can be used to predict the interactions between atoms.

Biochemical Significance of Weak Interactions

These interactions are crucial for stabilizing biological macromolecules and facilitating ligand binding
Weak interactions are reversible and easily broken.

Affects of Solutes On Properties Of Water

Colligative properties, like boiling point, melting point, and osmolarity, depend only on the number of solute particles but not their nature.
Noncolligative properties like viscosity, surface tension, taste, and color depend on the chemical nature of the solute.
Intracellular concentration can be high resulting in high osmotic pressure.

Ionization of Water

Water molecules are polar and can dissociate into protons (H+) and hydroxide ions (OH−).
Water dissociation is a rapid, reversible process.

lonization of Water - Quantitative Treatment

The concentrations of species are related through the equilibrium constant, K.
The ion product of water (Kw) is a constant at a set temperature.
Pure water has equal concentrations of H+ and OH-.

pH and Buffer Systems

Intracellular pH maintenance is crucial for cell survival and enzyme activity.
Buffer systems in living organisms, primarily based on phosphate, bicarbonate, and histidine.

Amino Acids and Peptides

Proteins within living organisms are constructed from a common set of 20 amino acids
each amino acid has a distinctive side-chain that determines its chemical properties
amino acids share a common structure that consists of: a central carbon ( ), four substituents (carboxyl group, amino group, hydrogen atom, and a unique R-group). Glycine has two hydrogens substituted for the R group
amino acids are named according to the standard nomenclature
amino acid residues that are constituents of proteins are L-stereoisomers
Histidine can form histamine.

Amino Acid Residues in Proteins

Protein amino acid residues are L-stereoisomers.
Proteins generally are designated as enantiomers; they are optically active and are distinguished by D or L nomenclature based on the configuration of chiral centers
These molecules exhibit different chemical properties to other enantiomers thereby affecting the physical and biological function of the molecule.

Peptides: Functional Roles

Peptides have diverse functions such as acting as hormones, neurotransmitters, antibiotics, and toxins.

Estimating the Number of Amino Acid Residues in Protein

Number of amino acid sequence residues calculated by dividing an estimated molecular weight of a protein by a typical average amino acid molecular weight (110).

Proteins Containing Chemical Groups Other Than Amino Acids

Conjugated proteins have non-amino acid parts called prosthetic groups
Lipoproteins contain lipids; glycoproteins contain sugars, and metalloproteins contain various specific metals.

Specific Activity

Specific activity is a measure of protein purity.
It's calculated by dividing protein activity by the total protein concentration.

Sequential Purification Steps

Steps in the purification process typically decrease the sample size
final specific activity:starting specific activity ratio = purification factor.

Protein Structure: Primary Structure

Proteins' primary structure is the sequence of amino acids in a polypeptide chain.
Covalent bonds link amino acid residues in the polypeptide chain.

Protein Structure: Secondary Structure

Secondary structure refers to recurring structural patterns in amino acid sequences.
Recurring structural patterns are observed including alpha-helices, beta-conformation, beta-turn, and random coils.

Protein Structure: Tertiary Structure

Proteins' tertiary structure represents the overall three-dimensional arrangement of all of the atoms in a protein.
Interaction between different segments of the polypeptide chain cause folding into the protein's three-dimensional shape.

Protein Structure: Quaternary Structure

Proteins' quaternary structure refers to the arrangement of two or more separate polypeptide chains in a three-dimensional complex.

Protein Structure: General Aspects

Proteins' structure determines its function; an amino-acid sequence will result in a determined 3D structure.

Protein Structure: Overview

Protein structures are stabilized by noncovalent interactions and forces (including: hydrophobic effect, hydrogen bonds, ionic bonds, and van der Waals forces).

Protein Conformations: Classification

Proteins can assume numerous conformations.
Proteins are most stable in a conformation where their free energy is low
These functional folded conformations are called native conformations .

A Protein's Conformation: How it's Stabilized

Protein conformation is mainly stabilized by numerous weak non-covalent interactions
These interactions include: hydrogen bonds, hydrophobic effect, and ionic interactions.

Packing of Hydrophobic Amino Acids in Proteins

Hydrophobic effect is the predominant weak interaction that predominates in the process of protein folding
A highly structured shell of water molecules (solvation layer) surround the hydrophobic molecule
When hydrophobic amino acid groups are clustered together the solvation layer decreases resulting in a favorable increase in the net entropy.

Polar Groups in Protein Folding

Some amino acid groups that are involved in protein folding include; acidic, basic, and polar groups
polar amino acid groups contribute to hydrogen bonding and salt bridge formation within a protein's structure

Individual Van der Waals Interactions

Individual van der Waals are relatively weak interactions
However; a large number of these interactions can have a significant overall contribution to stability in a protein structure

The Peptide Bond in Proteins

The peptide bond, a covalent bond is relatively rigid.
Bonds separate carbons of adjacent amino acids which create structural rigidity .

Peptide C-N Bonds

C-N bonds in peptides can not rotate freely.
Bonds' partial double-bond character constraints the range of different conformations.

Dihedral Angles and Peptide Conformations

Peptide conformations are defined by dihedral angles (φ, ψ, ω)
The range of φ and ψ angles are approximately -180 to +180 degrees.
The ω angle is ±180 degrees for trans peptide bonds and is 0 degrees for cis peptide bonds (rare).

Prohibited Conformations

Certain φ and ψ values are prohibited due to steric interference.
In fully extended polypeptides these are 180 degrees.

Classifying Proteins

Proteins are classified into fibrous, globular, membrane, and intrinsically disordered proteins based on their shapes and polypeptide chains

Fibrous Proteins

These are adapted for structural functions and give strength or flexibility to structures; example: a-keratin in hair, silk fibroin, collagen.

a-Keratin in Hair

a-keratin contains polypeptide chains oriented in parallel; those will wrap about one another forming a supertwisted coiled-coil

Hair Structure

Hair contains many a-keratin filaments, enriched with hydrophobic amino acids (Ala, Val, Leu, Ile, Met, Phe).
a-keratin filaments are connected by disulfide bonds.

Chemistry of Permanent Waving

The disulfide bonds of cysteine amino acids can be reduced and reoxidized to change the shape of a-keratin filaments.

Collagen Structure

Collagen is found in connective tissues with a repeating tripeptide unit.
The tripeptide units Gly-X-Y, where X is often Pro and Y is often 4-Hyp, result in a left-handed helix.
Collagen's tertiary structure is formed by three separate polypeptide chains that have right-handed twisting.

Some Proteins Undergo Assisted Folding

Some proteins require chaperone proteins to facilitate their folding
Some proteins can't fold spontaneously
These proteins might require chaperonins that are essential for folding.

Protein Folding Defects

Some protein folding disorders lead to amyloidosis diseases like; Alzheimer's, type 2 diabetes, and Huntington diseases.

Amyloid Fibrils

Amyloid fibers are formed when proteins are secreted in misfolded states.
They become insoluble extracellular fibers and aggregate causing disorder
Amyloid fibrils involve aggregation causing disorders.

Neurodegenerative Conditions

Neurodegenerative conditions such as; Alzheimer's, Parkinson's, and Huntington disease are largely caused by misfolded proteins due to defects in protein folding.

Cystic Fibrosis Defects

Cystic fibrosis results from the deletion of a phenylalanine residue resulting in improper protein folding
CFTR causes improper protein folding.

Prion Protein Misfolding

Prion protein (PrP) misfolding causes brain disorders
Misfolded brain proteins can cause neurological disorders.

Protein Functions: Classifications

Globular proteins serve various roles in storage, transport, defense, muscle contraction, and catalysis (e.g., myoglobin, hemoglobin, antibodies).

Protein Function: Interacting Dynamically with Other Molecules

Proteins function through interactions with other molecules.
Some reactions are catalyzed by proteins, enzymes which will alter chemical configuration or composition of the bound molecule
Other reactions do not alter the bound-molecule's composition or configuration.

Reversible Binding of Protein to a Ligand

Ligands can bind to proteins reversibly
Ligands are any molecules that bind to a protein.
Ligand interactions with proteins are critical to life, allowing rapid and reversible response to changing environmental and metabolic situations.

Oxygen Binding Proteins

Oxygen is poorly soluble in aqueous solutions
Transition metals have a high tendency to bind to O2, however, none of the 20 proteinogenic amino-acids can directly bind to O2.

Heme Prosthetic Group

Heme is a protein-bound prosthetic group present in myoglobin and hemoglobin
Heme contains a complex organic ring structure protoporphyrin, with a bound Fe2+ atom

Coordination Bonds of Iron

Iron atoms in heme have six coordination bonds
Four coordination bonds are to nitrogen atoms in the porphyrin ring
Two coordination bonds are perpendicular to the porphyrin ring.

Graphical Representations of Ligand Binding

The ligand-binding sites is often expressed as the fraction of binding sites occupied, Y, and as a function of the ligand concentration, [L].
The half-maximal binding is equal to 1/Kd.

Dissociation Constant

The dissociation constant (Kd) is the equilibrium constant for the release of a bound ligand.
A lower Kd represents a higher ligand affinity.
When the concentration of Ligand is equal to the dissociation constant the ligand binding sites are occupied by half
The value of the dissociation constant (Kd) determines the affinity.

Allosteric Proteins

Allosteric proteins have multiple binding sites where the binding properties of each site are modulated by other ligands that bind to another site on the same protein.
Ligands that bind to an allosteric protein to induce conformational change are called modulators.
Modulators are identified as homotropic modulators if they are identical to the normal ligands or heterotropic modulators if the modulator is different from normal ligand that is identified to interact with the protein.

Cooperative Ligand Binding

Cooperative ligand binding is a feature of proteins possessing multiple binding sites where the binding of one ligand affects the binding of other ligands to the protein
This means that binding of one ligand will affect binding to the other sites on the protein

Carbon Monoxide and Hemoglobin

Carbon monoxide (CO) has significantly higher affinity to Hemoglobin than oxygen (O2).
CO binding reduces the oxygen-carrying capacity of hemoglobin, causing toxicity.

The Bohr Effect

The structure effects of H+ and CO2 binding to hemoglobin will often favor the T state
These effects affect oxygen binding which, if a change occurs, is inversely related to O2 binding.
The Bohr effect is the effect pH and CO2 on the binding and release of O2 by hemoglobin.

Antibody-Antigen Interactions

Polyclonal antibodies are created by injecting a protein into an animal.
Polyclonal antibodies are produced by a mixture of antibodies that recognize different parts of the protein in question.
Monoclonal antibodies are prepared from a single population (clone) of identical B-cells.
Monoclonal antibodies are homogenous where each recognizes the same epitope.

Enzymes: Introduction & Classification

Enzymes are biological catalysts that greatly enhance reaction rates without affecting the equilibrium.
Enzymes are classified into seven classes (Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases, and Translocases) based on the type of reactions they catalyze.

Enzymes: Catalytic Activity & Chemical Components

The catalytic activity of an enzyme depends largely on its specific conformation as well as the coenzymes and cofactors; molecules (like metal ions, organic molecules) that contribute to its catalytic function and specific structure.
A holoenzyme is the entire combined molecule from an apoenzyme and its coenzyme/metal ion(s).

Enzymes: How They Work

Enzymes use active sites which are generally pockets in the enzyme (similar to ligand sites) in which substrates bind to undergo reactions to become a product.

Ground State and Transition State

Ground state = starting point when a reaction begins to occur
Transition state = the specific point between the ground state and the product state where molecules in the reaction are equally likely to form either product or begin returning to the reactant form
Energy changes in reaction are usually studied through a ground-state reaction-coordinate diagram, where energy values are plotted against the reaction-coordinate. Activation energy in reaction-coordinate diagrams graphically represents the energy required to reach a transition-state.

Rate Constants & Activation Energies

Enzyme activity can be studied and graphically represented by rate constants and activation energies
The relation between rate constant and activation energy is inverse and exponential
Lower activation energy corresponds to a faster reaction rate

Reaction Intermediates

Reaction Intermediates = any species that occurs on a reaction pathway with a finite lifetime
Examples include; enzyme-substrate (ES) complexes or enzymes-substrate-product (EP) complexes

Rate-Limiting Steps

Rate-limiting steps are the steps in a reaction that have highest activation energy that controls the reaction's overall rate.
Reaction rates have energy barriers that are related to activation energies

The Role of Binding Energy

The sum of the unfavorable energy from activation and the favorable binding energy of the ligand drives the reaction and results in a lower reaction activation energy.
Enzyme's substrate weak binding interactions drive enzymatic catalysis

The Active Site of an Enzyme, The Active Site's Role

Optimized binding energy, in a transition state, is accomplished by positioning a substrate in a cavity (the active site)
The active site of an enzyme is the region in an enzyme where a substrate binds

Enzyme Specificity

The enzyme's specificity arises from the optimized weak interactions between the enzyme and its specific substrate
The specificity is controlled by the shape of the active site that will specifically react with its substrate and not a similar competing molecule

Binding Energy overcoming the Barrier to Reactions

The barrier to reaction, which is an activation energy, includes: the entropy of the molecules, the solvation shell (water hydrogen-bonds with the molecule surrounding it), distortion of the substrate for reaction to occur and also alignment of catalytic groups on the enzyme.

Rate Enhancement by Entropy Reduction

This is determined by the restrictions of the substrate molecules, which also influence the orientation needed for the reaction that takes place.
Binding energy of the substrate affects the orientation for the reaction.
Enzyme reactions are highly specific due to the characteristics of entropy reduction and binding energies

Desolvation of the Substrate

Removal of the solvation shell (H2O surrounding the substrate) is called desolvation and is usually a negative contributor to the energy needed to reach a transition state
The weak interactions between enzyme and substrate largely influence desolvation and will overcome the unfavorable reaction energy changes

The Induced Fit Mechanism

Induced fit refers to the mechanism where enzymes undergo conformational changes by multiple weak interactions with substrate molecules to increase their efficiency and activity

Enzyme Kinetics

Enzyme kinetics is the branch of study that is focused on determining the rate of a chemical reaction and how changes in kinetics are observed upon changing experimental parameters

Factors Affecting Enzymatic Activity

Enzyme activity can be affected by substrate concentration and enzyme concentration, temperature and pH .

Substrate Concentration

Pre-steady state is the initial transient period before the reaction rate reaches a steady state
During pre-steady state, enzyme-substrate complexes form and increase to a constant level
Steady state period is the period after pre-steady when the enzyme-substrate complexes and other intermediates remain constant

Initial Velocities & Rates of Enzymes

Initial velocities or initial rates (V0) are measured from the beginning of the reaction and assumed to be at a constant substrate concentration
The observed rate is usually a measure of the steady-state and will be a measure of the reaction rate

The Michaelis-Menten Equation

Describes the relationship between substrate concentration ([S]) and reaction rate (V0)
The equation consists of the maximum velocity, Vmax, and Km the Michaelis Constant

Deriving The Michaelis Menten Equation

It is a simplified method for describing the general reaction in enzyme actions
Two major steps are involved in creating this equation

A Double Reciprocal Plot

This graph represents the Michaelis-Menten relationship as a linear form
This linear plot makes calculation of Km and Vmax more straightforward

Interpreting Km, Vmax in Enzyme Activity/Reactions

Km can vary, based on what substrate an enzyme is working with
Vmax is an indication of when virtually all enzymes exist as ES complexes
Km is a measure of how well substrate binds to enzyme

The Dissociation Constant Kd

Kd is closely linked to the relationship between Km and Vmax
If k₂ is the rate-limiting step, Km simplifies to k_1/k₁ which is also the dissociation constant Kd of enzyme-substrate complexes
Kd represents a measure of enzyme-substrate affinity

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Description

This quiz focuses on the structural characteristics of proteins, particularly the α helix, and explores factors affecting its stability and function. Test your knowledge about amino acid sequences, backbone arrangements, and the forces that stabilize proteins. Perfect for students studying biochemistry or molecular biology.