Biochemistry: Protein Structure and Function
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Questions and Answers

Which of the following describes the amphoteric property of amino acids?

  • Amino acids can only act as bases.
  • Amino acids can only act as acids.
  • Amino acids can act as both acids and bases. (correct)
  • Amino acids cannot donate or accept protons.

    • Which process involves the reaction between different amino acids to form peptides?

  • Peptidyl transfer (correct)
  • Deamination
  • Hydrolysis
  • Transamination

    • What is a key characteristic of essential amino acids?

  • They are identical in structure to non-essential amino acids.
  • They can be synthesized by the body.
  • They are not involved in protein synthesis.
  • They must be obtained through diet. (correct)

    • Which level of protein structure is characterized by the 3D arrangement of its polypeptide chains?

    <p>Tertiary structure</p> Signup and view all the answers

    What is the outcome of protein hydrolysis?

    <p>Breakdown into amino acids</p> Signup and view all the answers

    Which of the following is an example of a function related to protein structure?

    <p>Catalysis of biochemical reactions</p> Signup and view all the answers

    Which amino acid reaction is primarily involved in converting amino groups into urea?

    <p>Oxidative deamination</p> Signup and view all the answers

    What distinguishes denaturation from hydrolysis of proteins?

    <p>Denaturation disrupts proteins' 3D structures without breaking peptide bonds.</p> Signup and view all the answers

    What is the significance of proteins in the body?

    <p>They serve as the primary macromolecule accounting for 15% of total cell mass.</p> Signup and view all the answers

    What connects amino acids to form proteins?

    <p>Peptide bonds</p> Signup and view all the answers

    What misconception did physiologists have about proteins during their early studies?

    <p>Proteins could not be broken down into amino acids.</p> Signup and view all the answers

    Which of the following amino acids groups are categorized as Standard Amino Acids in humans?

    <p>Only 20 amino acids.</p> Signup and view all the answers

    What does the term 'proteios' refer to in the context of protein nomenclature?

    <p>First importance</p> Signup and view all the answers

    What is a characteristic feature of proteins as described?

    <p>They consist of unbranched polymer chains of amino acids.</p> Signup and view all the answers

    What percentage of a cell's dry weight is accounted for by proteins?

    <p>50%</p> Signup and view all the answers

    Who coined the term 'protein' and when?

    <p>Jacob Berzelius in 1839</p> Signup and view all the answers

    In which kind of solution does the amino acid primarily exist in its positively charged form?

    <p>Acidic solution</p> Signup and view all the answers

    Which statement best describes a zwitterion form of an amino acid?

    <p>It has both positive and negative charges but overall is neutral.</p> Signup and view all the answers

    What happens to an amino acid as the pH of the solution increases?

    <p>It switches from zwitterion to negatively charged form.</p> Signup and view all the answers

    What is the role of OH- ions in the ionization of amino acids?

    <p>They help transition amino acids to their negative ion form.</p> Signup and view all the answers

    Which of the following amino acid forms is dominant in a basic solution?

    <p>Negatively charged form</p> Signup and view all the answers

    Which representation correctly shows the amino acid form in a neutral pH solution?

    <p>H3N+ - C - COO-</p> Signup and view all the answers

    What does the R group of a standard amino acid represent?

    <p>A specific amino acid's side chain that varies among different amino acids.</p> Signup and view all the answers

    In an acidic solution, which of the following correctly depicts the state of alanine?

    <p>H3N+ – C – COOH</p> Signup and view all the answers

    At what pH does aspartic acid exist primarily as a zwitterion?

    <p>2.95</p> Signup and view all the answers

    What is the significance of the isoelectric point (pI) for an amino acid?

    <p>It is the pH at which the amino acid has no net charge.</p> Signup and view all the answers

    How can the isoelectric point (pI) of aspartic acid be calculated?

    <p>Using the sum of pKa1 and pKa2 divided by 2.</p> Signup and view all the answers

    What happens to the concentration of the negative ion form of aspartic acid at pH values above 3.9?

    <p>It predominates over the zwitterion form.</p> Signup and view all the answers

    What is the role of a buffer solution in paper electrophoresis?

    <p>To control the charge state of the amino acids.</p> Signup and view all the answers

    What property of amino acids allows them to be separated using electrophoresis?

    <p>Their charge at specific pH levels.</p> Signup and view all the answers

    Which two pKa values are relevant for calculating the isoelectric point of aspartic acid?

    <p>2.09 and 3.86</p> Signup and view all the answers

    What does the intermediate pH form of aspartic acid signify at pH 9.9?

    <p>The concentrations of its intermediate form and negative ion are equal.</p> Signup and view all the answers

    What term is used to describe an enzyme that is catalytically inactive due to the absence of its cofactor?

    <p>Apoenzyme</p> Signup and view all the answers

    Which of the following best describes the function of coenzymes?

    <p>They are often derived from vitamins.</p> Signup and view all the answers

    What classification of enzymes catalyzes oxidation and reduction reactions?

    <p>Oxidoreductases</p> Signup and view all the answers

    What is the significance of the '-ase' suffix in enzyme names?

    <p>It denotes that the molecule acts as an enzyme.</p> Signup and view all the answers

    What type of coenzyme is tightly bound to an enzyme?

    <p>Prosthetic group</p> Signup and view all the answers

    Which enzyme would be classified as a hydrolase?

    <p>Lipase</p> Signup and view all the answers

    What type of reaction does a transferase enzyme typically catalyze?

    <p>They catalyze the transfer of a group of atoms.</p> Signup and view all the answers

    Which of the following enzymes is a digestive enzyme that has an older name?

    <p>Pepsin</p> Signup and view all the answers

    At pH 6, which of the following amino acids will migrate towards the anode during electrophoresis?

    <p>Aspartic acid</p> Signup and view all the answers

    What is the primary reason alanine and isoleucine do not migrate in the electrophoresis at pH 6?

    <p>They exist as zwitterions.</p> Signup and view all the answers

    Which amino acid will migrate towards the cathode at pH 6?

    <p>Arginine</p> Signup and view all the answers

    What effect does spraying ninhydrin solution have on the visualization of amino acids after electrophoresis?

    <p>It produces a violet coloration if amino acids are present.</p> Signup and view all the answers

    Which amino acid has the highest isoelectric point (pI) in the provided sample?

    <p>Arginine</p> Signup and view all the answers

    At pH 6, which ion form of aspartic acid is predominant?

    <p>Negative ion form</p> Signup and view all the answers

    How does the migration of alanine and isoleucine differ from that of aspartic acid and arginine at pH 6?

    <p>Alanine and isoleucine do not migrate, while aspartic acid and arginine do.</p> Signup and view all the answers

    If the pH buffer was changed to 10, which amino acid would most likely not migrate towards the anode?

    <p>Arginine</p> Signup and view all the answers

    Study Notes

    Amphoteric Property of Amino Acids

    • Amino acids are amphoteric, meaning they can act as both acids and bases
    • This duality arises from the presence of both a carboxyl (-COOH) group and an amino (-NH2) group within their structure
    • The carboxyl group can donate a proton (H+), acting as an acid, while the amino group can accept a proton, acting as a base

    Peptide Formation

    • The formation of peptides involves a reaction between the carboxyl group of one amino acid and the amino group of another amino acid
    • This reaction, known as a dehydration reaction, releases a molecule of water and forms a peptide bond.

    Essential Amino Acids

    • Essential amino acids cannot be synthesized by the human body and must be obtained from the diet
    • They are crucial for various bodily functions, including protein synthesis, tissue repair, and hormone production

    Protein Structure: Tertiary Structure

    • Tertiary structure refers to the three-dimensional arrangement of a polypeptide chain, which is crucial for the protein's overall shape and function
    • This level of structure is stabilized by interactions between amino acid side chains, including hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions

    Protein Hydrolysis

    • Protein hydrolysis is the breakdown of proteins into their constituent amino acids through the addition of water
    • This process, usually catalyzed by enzymes, is essential for digestion and the recycling of amino acids within the body

    Function of Protein Structure

    • Protein structure dictates its function
    • Specific three-dimensional shapes enable proteins to interact with other molecules, facilitating a wide range of biological activities
    • Examples include enzymatic catalysis, transport of molecules, structural support, and signaling

    Urea Formation: Transdeamination

    • The conversion of amino groups into urea primarily involves transdeamination, a process involving the transfer of an amino group to α-ketoglutarate
    • This ultimately leads to the formation of urea, the primary waste product of nitrogen metabolism

    Protein Denaturation vs. Hydrolysis

    • Denaturation disrupts the secondary, tertiary, and quaternary structures of a protein, altering its three-dimensional shape without breaking peptide bonds
    • Hydrolysis, on the other hand, breaks peptide bonds, completely degrading the protein into its constituent amino acids

    Significance of Proteins

    • Proteins play critical roles in virtually every biological process, from structural support and enzymatic catalysis to transport and signaling
    • They contribute to cell growth, repair, and immune function

    Peptide Bond Formation

    • Peptide bonds are formed between the carboxyl group of one amino acid and the amino group of another
    • These bonds are responsible for linking amino acids together to form polypeptide chains, the building blocks of proteins

    Early Misconception about Proteins

    • Early physiologists mistakenly believed that proteins were the sole source of energy for the human body
    • This misconception was later corrected with the discovery of carbohydrates as the primary energy source

    Standard Amino Acids in Humans

    • Standard amino acids are the 20 amino acids commonly found in proteins of all living organisms
    • They include alanine (Ala), arginine (Arg), asparagine (Asn), aspartic acid (Asp), cysteine (Cys), glutamine (Gln), glutamic acid (Glu), glycine (Gly), histidine (His), isoleucine (Ile), leucine (Leu), lysine (Lys), methionine (Met), phenylalanine (Phe), proline (Pro), serine (Ser), threonine (Thr), tryptophan (Trp), tyrosine (Tyr), and valine (Val)

    'Proteios' and Protein Nomenclature

    • The term 'proteios' comes from the Greek word meaning "of primary importance," reflecting the fundamental role of proteins in biological systems
    • This term was used by Jöns Jacob Berzelius in the early 19th century to describe these complex organic molecules

    Characteristic Feature of Proteins

    • Proteins are large, complex polymers composed of amino acids linked by peptide bonds
    • They exhibit a wide variety of shapes and functions, crucial for all living organisms

    Protein Content in Cell Dry Weight

    • Proteins typically account for a significant portion of a cell's dry weight, often around 50%
    • This highlights the abundance and importance of proteins in cellular processes

    Coining of the Term 'Protein'

    • Jöns Jacob Berzelius, a Swedish chemist, coined the term "protein" in 1838
    • This term was chosen to reflect the essential nature of these molecules for living organisms

    Amino Acid in Positively Charged Form

    • In highly acidic solutions (low pH), amino acids primarily exist in their positively charged forms
    • This is because the carboxyl group is protonated (-COOH)
    • The amino group is also protonated (-NH3+), contributing to the overall positive charge

    Zwitterion Form of an Amino Acid

    • A zwitterion is a molecule with both a positive and a negative charge, but an overall neutral charge
    • In amino acids, the zwitterion form exists at a specific pH, typically near the isoelectric point
    • At this pH, the carboxyl group is deprotonated (-COO-) and the amino group is protonated (-NH3+), resulting in a neutral net charge

    Amino Acid Behavior with pH Increase

    • As the pH of a solution increases (becomes more basic), an amino acid undergoes deprotonation
    • The carboxyl group loses its proton, transitioning from -COOH to -COO-
    • At sufficiently high pH, the amino group may also deprotonate, transitioning from -NH3+ to -NH2

    Role of OH- Ions in Amino Acid Ionization

    • OH- ions, present in basic solutions, can react with the protonated carboxyl group (-COOH), removing the proton and forming water (H2O)
    • This process contributes to the deprotonation of the carboxyl group, leading to the formation of the carboxylate anion (-COO-)

    Amino Acid Form in Basic Solutions

    • In basic solutions (high pH), amino acids primarily exist in their negatively charged forms
    • This is due to the deprotonation of both the carboxyl group (-COO-) and the amino group (-NH2)

    Amino Acid Representation in Neutral pH

    • In a neutral pH solution, amino acids typically exist as zwitterions
    • This representation shows both the carboxyl group as a negatively charged carboxylate (-COO-) and the amino group as a positively charged ammonium ion (-NH3+)

    R Group of a Standard Amino Acid

    • The R group (also called the side chain) represents the variable portion of an amino acid
    • It is attached to the central carbon atom and determines the chemical properties of the amino acid
    • R groups can be hydrophobic, hydrophilic, acidic, basic, or polar, contributing to the diversity of amino acids and their unique roles in protein structure and function

    Alanine in Acidic Solution

    • In an acidic solution, the carboxyl group of alanine will be protonated (-COOH) and the amino group will be protonated (-NH3+)
    • This results in a positively charged alanine molecule
    • Alanine will exist as a cation in acidic solutions

    Aspartic Acid zwitterion form

    • Aspartic acid primarily exists as a zwitterion at a pH of approximately 2.9
    • This is because its isoelectric point (pI) is around 2.9

    Isoelectric Point (pI)

    • The isoelectric point (pI) is the pH at which an amino acid or protein carries no net electrical charge
    • At the pI, the amino acid exists as a zwitterion
    • The pI value is significant for separating and purifying amino acids and proteins using electrophoresis

    Calculating the pI of Aspartic Acid

    • The pI of aspartic acid can be calculated as the average of the two pKa values associated with the carboxyl groups
    • The pKa values for aspartic acid are approximately 2.1 and 3.9
    • pI = (2.1 + 3.9) / 2 = 3

    Negative Ion Form of Aspartic Acid at pH above 3.9

    • At pH values above 3.9, which is the pI of aspartic acid, the concentration of the negatively charged form of aspartic acid will increase
    • This is because the carboxyl group loses its proton, transitioning from -COOH to -COO-

    Buffer Solution in Paper Electrophoresis

    • A buffer solution is used in paper electrophoresis to maintain a constant pH
    • This is crucial for ensuring consistent and reliable separation of amino acids based on their charges

    Separating Amino Acids using Electrophoresis

    • Electrophoresis separates molecules based on their charge and size using an electric field
    • The net charge of an amino acid at a specific pH determines its migration direction in the electric field
    • Positively charged amino acids will migrate towards the negative electrode (cathode), while negatively charged amino acids will migrate towards the positive electrode (anode)

    pKa Values for Isoelectric Point Calculation of Aspartic Acid

    • The two pKa values relevant for calculating the isoelectric point (pI) of aspartic acid are:
      • The pKa value of the α-carboxyl group (approximately 2.1)
      • The pKa value of the side chain carboxyl group (approximately 3.9)

    Aspartic Acid at pH 9.9

    • At pH 9.9, aspartic acid will exist primarily as a negatively charged species
    • This is because both the α-carboxyl group and the side chain carboxyl group will be deprotonated (-COO-)

    Apoenzyme Definition

    • An apoenzyme refers to an enzyme that is catalytically inactive in the absence of its cofactor
    • It represents the protein component of a holoenzyme, lacking the non-protein component required for full enzymatic activity

    Function of Coenzymes

    • Coenzymes act as non-protein organic molecules that bind to enzymes and assist in catalyzing reactions
    • They often act as carriers of electrons, functional groups, or atoms, contributing to the enzyme's catalytic activity

    Oxidation-Reduction Enzymes

    • Oxidoreductases are a class of enzymes specifically responsible for catalyzing oxidation-reduction reactions
    • These reactions involve the transfer of electrons or hydrogen atoms between molecules

    '-ase' Suffix in Enzyme Names

    • The '-ase' suffix is commonly used to indicate an enzyme
    • This naming convention helps distinguish enzymes from other types of proteins

    Tightly Bound Coenzyme

    • A prosthetic group is a type of coenzyme tightly bound to an enzyme
    • It is essential for the enzyme's activity and cannot be easily removed

    Hydrolase Enzyme Example

    • Lipases are classified as hydrolases
    • They catalyze the breakdown of lipids (fats) by adding water to break the ester bonds

    Transferase Enzyme Reaction

    • Transferases typically catalyze the transfer of a functional group from one molecule to another
    • Examples include kinases, which transfer phosphate groups

    Digestive Enzyme with Older Name

    • Pepsin, a digestive enzyme responsible for protein breakdown in the stomach, is known by its older name, pepsin
    • This reflects its historical significance and its role in the digestive process

    Amino Acid Migration at pH 6

    • At pH 6, aspartic acid and arginine will migrate towards the anode (positive electrode) due to their net positive charge
    • Alanine and isoleucine will not migrate due to their neutral charge at this pH
    • Lysine will migrate towards the cathode (negative electrode) because it carries a net positive charge

    Reason for Alanine and Isoleucine Non-Migration

    • Alanine and isoleucine do not migrate in the electrophoresis at pH 6 because their isoelectric points are close to 6
    • This means they have a near-neutral charge at this pH, resulting in minimal movement in the electric field

    Amino Acid Migration Towards the Cathode at pH 6

    • Lysine will migrate towards the cathode (negative electrode) at pH 6 because its pI is greater than 6
    • This means it will have a net positive charge at pH 6, causing it to move towards the negative electrode

    Ninhydrin Solution Effect on Visualization

    • Spraying ninhydrin solution after electrophoresis reacts with amino acids, producing a purple color that allows visualization
    • This color reaction makes it easier to identify and analyze the separated amino acids

    Amino Acid With Highest pI

    • In the provided sample, lysine has the highest pI (pI = 9.7)
    • This indicates that lysine will exist as a zwitterion at a more basic pH compared to the other amino acids

    Aspartic Acid Ion Form at pH 6

    • At pH 6, aspartic acid will exist primarily in its negatively charged form
    • This is because its pI is around 2.9, and at pH 6, it will be deprotonated

    Difference in Migration of Amino Acids

    • At pH 6, aspartic acid will migrate towards the anode (positive electrode), while alanine, isoleucine, and lysine will exhibit different migration patterns
    • Alanine and isoleucine will not migrate since their pI is close to 6
    • Lysine will migrate towards the cathode (negative electrode) due to its higher pI

    Amino Acid Not Migrating Towards Anode at pH 10

    • At pH 10, aspartic acid, which has a pI of around 3, will likely be negatively charged and migrate towards the anode
    • The other amino acids might migrate differently, depending on their individual pI values
    • It is important to note that all amino acids, including aspartic acid, can be negatively charged under very basic conditions (high pH values)

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    Test your knowledge of proteins and amino acids in this quiz focused on their structures, functions, and properties. Explore key concepts like amphoteric properties, protein hydrolysis, and essential amino acids. Perfect for biochemistry students looking to reinforce their understanding.

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