Amino Acids: Protein Fundamentals

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Questions and Answers

What is the primary role of proteins in a cell?

To protect the cell from pathogens

To store energy

To provide structural support

To mediate virtually every process (correct)

Which property is NOT typically associated with amino acids?

Ability to conduct electricity (correct)

Capacity to polymerize

Useful acid-base properties

Diverse chemical functionality

Which amino acid does not follow the standard structure of amino acids?

Serine

Glycine

Proline (correct)

Alanine

What does the designation L/D of amino acids refer to?

The configuration of substituents around the chiral carbon Signup and view all the answers

What is the average molecular weight (MW) of the amino acids in proteins?

128 Signup and view all the answers

Which statement about amino acids is correct?

L-amino acids are the only form found in proteins. Signup and view all the answers

Which type of amino acids is characterized by non-polar side chains?

Non-polar amino acids Signup and view all the answers

What characteristic allows certain amino acids to absorb UV light?

Presence of aromatic rings Signup and view all the answers

At a physiological pH of 7.4, how are polar basic side chain amino acids typically charged?

Fully protonated Signup and view all the answers

Which amino acid is specifically known to form disulfide bonds?

Cysteine Signup and view all the answers

Which of the following is true about polar acidic amino acids at physiological pH?

They are fully ionized and negatively charged. Signup and view all the answers

Which amino acid is commonly found as part of the structure in collagen?

Glycine Signup and view all the answers

What is a defining feature of amphiphilic amino acids?

They contain both polar and non-polar regions. Signup and view all the answers

What unique property differentiates one of the uncommon amino acids compared to lysine?

One less methylene group Signup and view all the answers

What is the primary reason that peptide bonds can last more than 1,000 years in the absence of a catalyst?

They have a very low tendency to hydrolyze without a catalyst. Signup and view all the answers

Which terminal group contributes to the isoelectric point (pI) of a peptide?

Both the amino and carboxyl groups Signup and view all the answers

Which of the following is not considered a prosthetic group?

NAD+ in lactate dehydrogenase Signup and view all the answers

What is the main concept behind using electrophoresis for protein separation?

Proteins move according to their charge in an electric field. Signup and view all the answers

Which property is NOT commonly relied upon for the separation of proteins from a crude extract?

Flammability Signup and view all the answers

What would an amino acid with a pI of 9.7 do in a solution with a pH of 7.0?

It will have a net positive charge and move toward the negative electrode. Signup and view all the answers

What is the net charge of an amino acid at its isoelectric point (pI)?

0 Signup and view all the answers

Which amino acid structure contributes to the amphoteric nature?

None of the above Signup and view all the answers

What are the pKa values for amino acids with uncharged side chains typically used for?

Acting as buffers in solution Signup and view all the answers

What occurs at the pI of amino acids with ionizable side chains?

The amino acid is least soluble in water Signup and view all the answers

In terms of acidity, how does the alpha-carboxy group of amino acids compare to typical carboxylic acids?

It is more acidic. Signup and view all the answers

What determines the more complex titration curves for amino acids with ionizable side chains?

Distance between pKa values Signup and view all the answers

What is the general formula for calculating the isoelectric point (pI) for amino acids without ionizable side chains?

pK1 + pK2 Signup and view all the answers

What kind of bonds are formed during the synthesis of peptides from amino acids?

Covalent bonds Signup and view all the answers

What happens to the equilibrium of peptide synthesis compared to hydrolysis?

Equilibrium favors hydrolysis. Signup and view all the answers

What characteristic defines amino acids that can act as buffers in two distinct pH regimes?

Presence of both acidic and basic groups Signup and view all the answers

What is the approximate average molecular weight of a protein amino acid residue after accounting for water released in peptide bond formation?

110 Signup and view all the answers

Which amino acid is characterized as having an additional hydrogen as a fourth substituent on the alpha carbon?

Glycine Signup and view all the answers

How do the properties of amino acids contribute to their biological functions?

They exhibit diverse physical and chemical properties. Signup and view all the answers

Which statement regarding L amino acids in proteins is accurate?

Proteins are exclusively made of L amino acids. Signup and view all the answers

What role does the R group of an amino acid play in determining its properties?

It determines the amino acid's net charge in solution. Signup and view all the answers

What is a defining feature of proteins related to their composition of amino acids?

Proteins are assembled from a specific sequence of L amino acids. Signup and view all the answers

Which factor is NOT typically relied upon when separating proteins from crude extracts?

Color Signup and view all the answers

What role do cofactors play in conjugated proteins?

They assist in the enzyme's catalytic activity. Signup and view all the answers

At a pH of 7.0, what charge would an amino acid with a pI of 9.7 have?

Positive Signup and view all the answers

Which of the following is considered a prosthetic group?

NAD+ in lactate dehydrogenase Signup and view all the answers

Which method is commonly used for the preparative separation of proteins?

Chromatography Signup and view all the answers

What is the primary characteristic of hemoproteins?

They have heme as a prosthetic group. Signup and view all the answers

Which compound acts as the main inhibitory neurotransmitter in the central nervous system?

g-Aminobutyric Acid Signup and view all the answers

What is the charge of amino acids at a neutral pH?

Zwitterion form Signup and view all the answers

Which amino acid derivative is a precursor to catecholamines like dopamine and norepinephrine?

Dihydroxy Phenylalanine Signup and view all the answers

What happens to the amino group of an amino acid at alkaline pH?

It becomes neutral Signup and view all the answers

Which of the following statements about serotonin is correct?

It is primarily found in the central nervous system. Signup and view all the answers

Which compound is a precursor for Triiodothyronine (T3)?

Thyroxine T4 Signup and view all the answers

At acidic pH, which form do amino acids predominantly take?

Cationic form Signup and view all the answers

Which bio-active compound is a major neurotransmitter derived from the amino acid tryptophan?

Serotonin Signup and view all the answers

At the isoelectric point (pI), what is the net charge of an amino acid?

0 Signup and view all the answers

Which is the correct formula for calculating the isoelectric point (pI) for amino acids without ionizable side chains?

pI = (pK1 + pK2) / 2 Signup and view all the answers

What happens to amino acids at a pH value close to their pKa values?

They exist predominantly as zwitterions. Signup and view all the answers

What structural feature distinguishes amino acids that can act as buffers in solution?

Presence of an ionizable side chain. Signup and view all the answers

Why are the titration curves of amino acids with ionizable side chains more complex?

Their side chains significantly affect pKa values. Signup and view all the answers

Which of the following statements about amino acids' pKa values is accurate?

pKa values indicate the strength of acidic or basic groups. Signup and view all the answers

How does the presence of both COOH and NH2 groups in amino acids affect their behavior in solution?

They can contribute to the formation of zwitterions. Signup and view all the answers

What is a characteristic of peptides as compared to proteins?

Peptides are simpler condensation products of amino acids. Signup and view all the answers

What is the chemical behavior of amino acids at their isoelectric point (pI)?

They are least soluble in water. Signup and view all the answers

Study Notes

Amino Acids: Building Blocks of Protein

Proteins are polymers comprised of amino acids.
Amino acids are well-suited for biological functions due to their ability to polymerize, their acid-base properties, and their diverse physical properties and chemical functionalities.
Most amino acids share common structural features and are chiral with a tetrahedral 𝞪-carbon.
All amino acids except proline have an acidic carboxyl group, a basic amino group, an 𝞪-hydrogen, and a fourth substituent (R).

Classification of Amino Acids

Amino acids can be classified based on the properties of their R groups.
Non-polar aliphatic R groups: Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Proline (Pro).
Aromatic R groups: Phenylalanine (Phe), Tyrosine (Tyr), Tryptophan (Trp).
Polar uncharged R groups: Serine (Ser), Threonine (Thr), Cysteine (Cys), Asparagine (Asn), Glutamine (Gln).
Polar positively charged R groups: Lysine (Lys), Arginine (Arg), Histidine (His).
Polar negatively charged R groups: Aspartic acid (Asp), Glutamic acid (Glu).

Uncommon Amino Acids

Some proteins contain uncommon amino acids such as 4-hydroxyproline in collagen, 𝞪-carboxyglutamate in prothrombin, and desmosine in elastin.

Amphoteric Nature of Amino Acids

Amino acids are amphoteric, meaning they can act as both acids and bases.
In solution, amino acids exist mainly as zwitterions, which have both a positive and negative charge.
The pKa values of the carboxyl and amino groups determine the pH at which the amino acid will have a net charge of zero (its isoelectric point).

Ionizable Side Chains

Amino acids with ionizable side chains can influence their pKa values and their behavior in solution, contributing to their overall charge.
The isoelectric point (pI) is calculated using the pKa values of the carboxyl, amino, and ionizable side chains.

Peptide Bond Formation

Peptides are formed through the condensation reaction between the carboxyl group of one amino acid and the amino group of another.
The formation of a peptide bond removes a water molecule.
The equilibrium of peptide bond formation favors hydrolysis, but peptide bonds are kinetically stable under physiological conditions.

Peptide Structure and Nomenclature

Peptides are named by listing the amino acids from the N-terminus (amino group) to the C-terminus (carboxyl group).
The sequence of amino acids is an important determinant of peptide structure and function.

Ionization of Peptides

Peptides can ionize due to the presence of terminal amino and carboxyl groups, as well as ionizable side chains.
Each peptide has a characteristic isoelectric point (pI).

Conjugated Proteins

Conjugated proteins contain non-amino acid components called cofactors, which are essential for their function.
Cofactors can be metal ions or organic molecules called coenzymes.
Some cofactors are covalently attached to the protein and are called prosthetic groups.
Different types of conjugated proteins include lipoproteins, glycoproteins, phosphoproteins, hemoproteins, flavoproteins, and metalloproteins.

Separation and Purification of Proteins

Protein purification involves separating proteins from a crude extract based on differences in their physical and chemical properties.
Common methods for protein separation include chromatography and electrophoresis.

Electrophoresis

Electrophoresis separates molecules based on charge and size using an electric field and a gel matrix.
The charge of a protein in electrophoresis is determined by the pH of the solution and the protein's pI.
A protein will migrate toward the cathode (negative electrode) if its pI is lower than the pH, and toward the anode (positive electrode) if its pI is higher than the pH.
Proteins in an electrophoresis gel are often stained with dyes to visualize them.

Protein Structure

Protein structure can be classified into four levels:
- Primary structure: the sequence of amino acids
- Secondary structure: local, repeating structures such as α-helices and β-sheets
- Tertiary structure: the three-dimensional conformation of a single polypeptide chain
- Quaternary structure: the arrangement of multiple polypeptide chains in a protein complex

Summary

This lecture covered the structure and properties of amino acids, peptides, and proteins, including their ionization behavior and methods of separation and purification.
Understanding these principles is fundamental to understanding protein function in biological systems.

Amino Acids: Building Blocks of Proteins

Proteins are linear heteropolymers of α-amino acids
Proteins mediate virtually every process in a cell
Amino acids have unique properties that enable a variety of biological functions:
- Capacity to polymerize
- Useful acid-base properties
- Diverse physical properties
- Diverse chemical functionality

α-Amino Acid Structure

Most α-amino acids share common structural features and are chiral.
The α-carbon always has four substituents and is tetrahedral.
All amino acids (except proline) have:
- An acidic carboxyl group
- A basic amino group
- An α-hydrogen connected to the α-carbon
- A fourth substituent (R), unique
  - In glycine, the fourth substituent is also hydrogen
  - R group can be quite complex

L-Amino Acids

Proteins only contain L-amino acids.
L/D represent the relative configuration of amino acids to L- and D-glyceraldehyde.

Average Molecular Weight of Amino Acids

The average molecular weight of all 20 amino acids is about 138.
However, there is a greater prevalence of low molecular weight amino acids in most proteins, so the average molecular weight of protein amino acids is closer to 128.
Subtracting 18 for water released upon peptide bond formation brings the average molecular weight of an amino acid residue to 110.
Dividing the molecular weight of a protein by approximately 110 gives the approximate number of amino acids in the protein.

Bioactive Compounds Derived from Amino Acids

Other important bio-active compounds are derived from amino acids:
- Serotonin
- GABA
- Catecholamines
- Dihydroxy Phenylalanine (DOPA)
- Thyroxine (T4)
- Triiodothyronine (T3)

Ionization of Amino Acids

At acidic pH, the carboxyl group is protonated and the amino acid is in the cationic form.
At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; such ions are called Zwitterions.
At alkaline pH, the amino group is neutral -NH2 and the amino acid is in the anionic form.

Amphoteric Nature of Amino Acids

Amino acids act as buffers in solution.
Amino acids with uncharged side chains, like glycine, have two pKa values:
- The pKa of the α-carboxyl group is 2.34.
- The pKa of the α-amino group is 9.6.
They can act as a buffer in two pH regimes.

Isoelectric Point (pI)

Amino acids carry a net charge of zero at a specific pH, which is the pI (Isoelectric Point).
Zwitterions predominate at pH values between the pKa values of the amino and carboxyl groups.
For amino acids without ionizable side chains, the pI is calculated as (pK1 + pK2) / 2.
At this point:
- The net charge is zero
- The least soluble in water
- No migration in an electric field

Chemical Environment Affecting pKa Values

The simultaneous presence of COOH and NH2 groups in amino acids:
- Makes the α-carboxy group much more acidic than in carboxylic acids.
- Makes the α-amino group slightly less basic than in amines.

Ionizable Side Chains in Titration Curves

Ionizable side chains can be titrated, making titration curves more complex.
pKa values are discernable if two pKa values are more than two pH units apart.
Examples:
- Monoamino monocarboxylic AA
- Monoamino dicarboxylic AA
- Diamino monocarboxylic AA
- Histidine

General Calculation of pI with Ionizable Side Chains

Identify the species that carries a net zero charge (Zwitter Ion).
Identify the pKa value that defines the acid strength of this Zwitter Ion.
Identify the pKa value that defines the base strength of this Zwitter Ion.
Take the average of these two pKa values.

Formation of Peptides and Proteins

Peptides:
- Small condensation products of amino acids.
- Considered "small" compared to proteins, which have a molecular weight greater than 10 kDa.
Equilibrium lies on the side of hydrolysis, so energy is needed to synthesize peptides.
Hydrolysis rates are slow, making peptide bonds kinetically stable.
In the absence of a catalyst in an aqueous environment, a peptide bond would last for more than 1,000 years.

Peptide Nomenclature

Numbering and naming starts from the amino terminus.
Example: H2N-Ser-Gly-Tyr-Ala-Leu-COOH

Ionization of Peptides

The terminal amino and carboxyl groups contribute to the pI, along with any ionizable R groups.
Peptides and proteins have characteristic pI values.

Conjugated Proteins

Some proteins contain other chemical compounds besides amino acids:
- Cofactors:
  - Functional non-amino acid component
  - Examples: metal ions, organic molecules (coenzymes)
- Coenzymes:
  - Organic cofactors
  - Example: NAD+ in lactate dehydrogenase
- Prosthetic groups:
  - Covalently attached cofactors
  - Example: heme in myoglobin

Classes of Conjugated Proteins

Lipoproteins: Lipids (example: β1-Lipoprotein of blood)
Glycoproteins: Carbohydrates (example: Immunoglobulin G)
Phosphoproteins: Phosphate groups (example: Casein of milk)
Hemoproteins: Heme (iron porphyrin) (example: Hemoglobin)
Flavoproteins: Flavin nucleotides (example: Succinate dehydrogenase)
Metalloproteins: Various metals (examples: Ferritin, Alcohol dehydrogenase, Calmodulin, Dinitrogenase, Plastocyanin)

Separation and Purification of Proteins

Source of proteins is diverse - tissues and individual cells.
Lysis is used to generate a crude extract.
Separation of proteins from crude extracts relies on differences in physical and chemical properties:
- Charge
- Size
- Affinity for a ligand
- Solubility
- Hydrophobicity
- Thermal stability
Chromatography commonly used for preparative separation.

Electrophoresis for Amino Acid or Protein Analysis

Separation done in analytical scale by electrophoresis:
- Electric field pulls amino acids or proteins according to their charge.
- Gel matrix hinders mobility of proteins based on size and shape.
- Samples loaded onto a gel matrix (polyacrylamide) along with molecular weight markers and controls (purified proteins).
- An electric field is applied.
- Gel is isolated and stained with dye.

Protein Structure

Three main levels of protein structure:
- Primary structure: Description of all covalent bonds, including disulfide bonds, and the amino acid sequence.
- Secondary structure: Particular stable arrangements of amino acid residues resulting in recurring patterns, such as α-helices and β-sheets.
- Tertiary structure: Arrangement in space of a protein, describing the 3-dimensional polypeptide folding.

Goals and Objectives

Understand the structure, properties, and naming of amino acids.
Understand the structure and properties of peptides and proteins.
Understand the ionization behavior of amino acids and peptides and the isoelectric point.
Be familiar with classes of conjugated proteins, cofactors, coenzymes, and prosthetic groups.
Know methods to separate and purify peptides and proteins, including electrophoresis of proteins and their behavior in an electric field.

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Description

Explore the fundamental building blocks of proteins through this quiz on amino acids. Test your knowledge on their classification, structural features, and functional properties. Perfect for students studying biochemistry or molecular biology.