Amino Acids and Nutrition

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Questions and Answers

What is the primary function of hydrogen bonds in secondary structure formation?

To create a random coil conformation

To share H-atoms between oxygen and nitrogen of different peptide bonds (correct)

To break down the polypeptide chain

To form covalent bonds between peptide bonds

What type of bonds are disulfide bridges?

Non-covalent bonds

Electrostatic interactions

Hydrogen bonds

Covalent bonds (correct)

What is the characteristic of a right-handed α-helix structure?

Parallel β-pleated sheet structure

Left-handed orientation

Intra-chain hydrogen bonds (correct)

Inter-chain hydrogen bonds

What is the main stabilization factor of tertiary structure in proteins?

Non-covalent bonds Signup and view all the answers

What type of β-pleated sheet structure is formed when adjacent polypeptide chains run in opposite directions?

Anti-parallel β-pleated sheet Signup and view all the answers

What is the main function of β-turn or β-bends in proteins?

To change the direction of a polypeptide chain Signup and view all the answers

What is the term for proteins containing two or more polypeptide chains?

Oligomers Signup and view all the answers

What is the function of disulfide isomerase in protein folding?

To break unwanted disulfide bonds Signup and view all the answers

What is the typical number of amino acids that make up a β-turn?

4 Signup and view all the answers

What is the role of chaperons in protein folding?

To prevent the formation of aggregates by binding to hydrophobic parts of protein molecules Signup and view all the answers

What is the term for regions of proteins that are not organized as helices and pleated sheets?

Random coil conformation Signup and view all the answers

What is the result of the joining of regions of α-helix and β-pleated sheet in some globular proteins?

Formation of a super secondary structure Signup and view all the answers

What is the term for the sequence of residues in a protein?

Primary structure Signup and view all the answers

What is the term for the complete folding pattern of a protein?

Tertiary structure Signup and view all the answers

What is the characteristic of hydrogen bonds in secondary structure?

Weak, low-energy noncovalent bonds Signup and view all the answers

What is the term for the interaction of subunits in a protein?

Quaternary structure Signup and view all the answers

What percentage of the total protein in mammals is collagen?

25% Signup and view all the answers

Which of the following is NOT a force involved in quaternary structure?

Covalent bonds Signup and view all the answers

What happens to a protein when it is denatured?

Its physical, chemical and biological properties are altered Signup and view all the answers

What is a common cause of denaturation of proteins?

High temperature Signup and view all the answers

What is the characteristic feature of fibrous proteins?

Axial ratio of length: width is more than 10 Signup and view all the answers

What is the function of collagen in the body?

To form the extracellular matrix Signup and view all the answers

What is the pKa value of NH3?

9.2 Signup and view all the answers

What is the function of cis-trans prolyl isomerase in protein folding?

To catalyze the interconversion of cis-trans peptide bonds of proline residues Signup and view all the answers

What is the pKa value of COOH?

2.3 Signup and view all the answers

Which of the following amino acids is semi-essential?

Histidine Signup and view all the answers

What is the number of enzymes required for the synthesis of arginine?

7 Signup and view all the answers

What is the function of taurine?

Bile acids Signup and view all the answers

Which of the following is not an essential amino acid?

Alanine Signup and view all the answers

What is the characteristic feature of collagen?

It is a triple helix of one or two different polypeptide chains Signup and view all the answers

Which of the following amino acids is involved in the urea cycle?

All of the above Signup and view all the answers

What is the characteristic of the collagen triple helix?

It has 3 amino acids per turn of the helix Signup and view all the answers

What percentage of collagen is composed of proline and hydroxyproline?

21% Signup and view all the answers

What percentage of collagen is composed of glycine?

33% Signup and view all the answers

What type of bonds are formed between hydroxylysine residues in collagen?

Covalent bonds Signup and view all the answers

What is the repeating pattern of amino acids in collagen?

(G-X-Y) repeats Signup and view all the answers

What is the function of collagenases?

To degrade collagen Signup and view all the answers

What is the function of γ-aminobutyric acid?

Neurotransmitter Signup and view all the answers

What is the primary structure of a collagen polypeptide chain?

A right-handed triple helix Signup and view all the answers

What type of interactions stabilize the conformation of collagen?

Hydrophobic interactions and hydrogen bonds Signup and view all the answers

What is the main goal of protein analysis in molecular medicine?

To identify proteins associated with specific physiologic states or diseases Signup and view all the answers

Which of the following techniques is used to determine the primary structure of a protein?

Edman's Method Signup and view all the answers

What is the purpose of highly purified protein?

To use in biological, medical, and pharmaceutical processes Signup and view all the answers

Which of the following is a method used in protein sequencing?

Sanger's Method Signup and view all the answers

What is the purpose of N-Terminal Analysis?

To determine the amino terminal end of a polypeptide chain Signup and view all the answers

What is Edman's Reagent used for in protein sequencing?

To cleave amino acids from a polypeptide chain Signup and view all the answers

Why is protein purification necessary?

To obtain highly purified protein for further analysis and use Signup and view all the answers

What is the purpose of Carboxypeptidase Method in protein sequencing?

To determine the carboxy terminal end of a polypeptide chain Signup and view all the answers

What is the main difference between N-Terminal Analysis and C-Terminal Analysis?

N-Terminal Analysis determines the amino terminal end, while C-Terminal Analysis determines the carboxy terminal end Signup and view all the answers

What is the purpose of protein sequencing?

To determine the amino acid sequence of proteins Signup and view all the answers

What type of interactions occur between proteins and the stationary phase in ion exchange chromatography?

Charge-charge interactions Signup and view all the answers

What is the primary mechanism of protein purification in affinity chromatography?

Specific binding to immobilized ligands Signup and view all the answers

What is the primary principle behind salt precipitation in protein purification?

Differences in protein solubility in response to ionic strength Signup and view all the answers

What is the purpose of adding salts such as ammonium sulfate in protein purification?

To separate proteins based on their degree of solubility Signup and view all the answers

What is the purpose of using urea, guanidine hydrochloride, or high salt concentrations in affinity chromatography?

To disrupt protein-ligand interactions Signup and view all the answers

What is the primary component of the stationary phase in paper chromatography?

Filter paper Signup and view all the answers

What is the characteristic of proteins that adhere to beads with negatively charged functional groups in ion exchange chromatography?

Net positive charge Signup and view all the answers

What is the purpose of using SDS in polyacrylamide gel electrophoresis (PAGE)?

To denature proteins Signup and view all the answers

What is the primary interaction between proteins and the stationary phase in column chromatography?

All of the above Signup and view all the answers

What is the primary advantage of using high pressure chromatography (HPLC)?

High resolution separation Signup and view all the answers

What is the purpose of the mobile phase in chromatography?

To percolate through the column and facilitate protein separation Signup and view all the answers

What is the basis of separation in size exclusion chromatography?

Shape and size Signup and view all the answers

What is the primary advantage of using multiple successive purification techniques in protein purification?

Increased protein purity Signup and view all the answers

What is the purpose of using different pH values in ion exchange chromatography?

To elute bound proteins Signup and view all the answers

What is the primary characteristic of proteins that are separated using salt precipitation?

Differences in solubility Signup and view all the answers

What is the advantage of using affinity chromatography compared to other chromatography methods?

High selectivity Signup and view all the answers

What is the primary component of the stationary phase in thin-layer chromatography?

All of the above Signup and view all the answers

What is the purpose of using immobilized substrates, products, or inhibitors in affinity chromatography?

To purify proteins based on their specific binding interactions Signup and view all the answers

What is the primary purpose of chromatographic techniques in protein purification?

To separate proteins based on their properties Signup and view all the answers

What is the primary mechanism of salt precipitation in protein purification?

Salting out of proteins Signup and view all the answers

Study Notes

Amino Acids

There are 20 different amino acids that occur naturally in proteins.
Essential amino acids cannot be synthesized by the human body and must be obtained from the diet.
Non-essential amino acids can be synthesized by the human body.
Examples of essential amino acids: methionine (M), arginine (A), tryptophan (T), threonine (T), valine (V), isoleucine (IL), leucine (L), phenylalanine (P), histidine (H), and lysine (L).
Histidine and arginine are sometimes referred to as semi-essential because the body synthesizes them to some extent.

Biosynthesis of Amino Acids

The biosynthesis of non-essential amino acids is different from that of essential amino acids.

Essential Amino Acids are Difficult to Synthesize

The number of enzymes required for the synthesis of essential amino acids is higher than that of non-essential amino acids.

Rare and Unusual Amino Acids

These amino acids are not found in proteins but play important roles in metabolism.
Examples: ornithine, citrulline, arginino succinic acid, β-alanine, taurine, γ-aminobutyric acid, mono- and di-iodotyrosine, pantothenic acid, homoserine, and homocysteine.

Secondary Structure

The folding of short segments of polypeptide into geometrically ordered units.
Hydrogen bonds are weak, low-energy noncovalent bonds formed between oxygen of CO and nitrogen of -NH of different peptide bonds.
Secondary structure can form either an α-helix or β-pleated sheet structure.

Alpha Helix Structure

Right-handed α-helix has intra-chain hydrogen bonds.

Beta Sheet Structure

Parallel β-pleated sheet is formed when adjacent polypeptide chains run in the same direction.
Anti-parallel β-pleated sheet is formed when adjacent polypeptide chains run in opposite directions.

Random Coil (Disordered) Conformation

Regions of proteins that are not organized as helices and pleated sheets are said to be present in random coil conformation.

Beta Turn (Reverse Turn)

A hairpin turn of a polypeptide chain is called a β-turn.
β-turn connects anti-parallel β-sheets and usually consists of four amino acids: Gly, Ser, Asp, and proline.

Super Secondary Structure

In some globular proteins, regions of α-helix and β-pleated sheet join to form super secondary structure or motifs.

Tertiary Structure

The three-dimensional folding of a polypeptide chain.
Tertiary structure is mainly stabilized by non-covalent bonds.

Non-Covalent Bonds in Tertiary Structure

Electrostatic interactions, hydrogen bonding, interactions of non-polar side chains, van der Waals interactions, and disulfide bridges (in some proteins) stabilize protein structure.

Quaternary Structure

Proteins containing two or more polypeptide chains possess quaternary structure.
These proteins are called oligomers, and the individual polypeptide chains are called protomers or subunits.

Forces in Quaternary Structure

Hydrogen bonding, electrostatic interactions, hydrophobic interactions, van der Waals interactions, and disulfide bonds stabilize quaternary structure.

Protein Folding

Protein folding enzymes: disulfide isomerase and cis-trans prolyl isomerase aid protein folding.

Protein Factors

Chaperones (chaperonins) aid protein folding by preventing the formation of aggregates.

Denaturation of Proteins

Denaturation is the loss of native conformation, and it alters physical, chemical, and biological properties of a protein.

Causes of Denaturation

High temperature, extreme pH, use of urea and guanidine at high concentrations, UV radiation, sonication, vigorous shaking, detergent treatment, and exposure to heavy metals can cause denaturation.

Classification of Proteins on the Basis of Shape and Size

Fibrous proteins have an axial ratio of length: width greater than 10.
Globular proteins have an axial ratio of length: width less than 10.

Structural Protein: Collagen

Collagen is the major protein comprising the extracellular matrix (ECM).
Collagen is mainly synthesized by fibroblasts, muscle cells, and epithelial cells.
There are about 28 different types of collagen.

Collagen Structure

Collagen consists of 3 coiled subunits (3 polypeptide chains-α chains).
Each chain consists of about 1000 amino acids twisted around each other in a characteristic right-handed triple helix.
Every third amino acid residue of collagen is glycine (Gly).

Protein Analysis

Protein structure can be analyzed using:
- X-ray crystallography
- Nuclear magnetic resonance (NMR)
- Spectroscopy
Protein activity and amount can be analyzed using:
- UV spectroscopy
- Bradford protein assay
- Coomassie brilliant blue dye

Determination of Protein Primary Structure (Amino Acid Composition)

Identification of proteins associated with specific physiologic states or diseases is an important goal of molecular medicine
Primary sequence of a protein provides a molecular fingerprint for identification and information for cloning the gene or genes that encode it

Protein Sequencing

N-Terminal analysis determines the amino terminal end of the polypeptide chain using:
- Sanger's method
- Edman's method
C-Terminal analysis determines the carboxy terminal end of the polypeptide chain using:
- Carboxypeptidase method
Edman's sequencing method involves:
- Chromatography
- Electrophoresis
- Spectroscopy

Protein Purification

Highly purified protein is essential for determining its amino acid sequence and for use in biological, medical, and pharmaceutical processes
Protein purification involves isolating a specific protein from a mixture of thousands of different proteins
Classic approaches use differences in target protein properties, such as:
- Salt precipitation (salting out)
- Chromatographic techniques

Chromatographic Techniques

Chromatographic separations partition molecules between two phases: mobile and stationary
Stationary phase matrices interact with proteins based on their:
- Charge
- Hydrophobicity
- Ligand-binding properties
Types of chromatography include:
- Ion exchange chromatography
- Size exclusion chromatography
- Affinity chromatography
- High pressure chromatography (HPLC)

Ion Exchange Chromatography

Proteins interact with the stationary phase by charge-charge interactions
Proteins with a net positive charge adhere to beads with negatively charged functional groups (cation exchangers)
Proteins with a net negative charge adhere to beads with positively charged functional groups (anion exchangers)

Affinity Chromatography

Affinity chromatography exploits the high selectivity of proteins for their ligands
Proteins can be purified using immobilized substrates, products, coenzymes, or inhibitors
Bound proteins are eluted by competition with soluble ligand or by disrupting protein-ligand interactions using:
- Urea
- Guanidine hydrochloride
- Mildly acidic pH
- High salt concentrations

SDS-PAGE

SDS-PAGE is a technique used to separate proteins based on their molecular weight
It involves polyacrylamide gel electrophoresis in the presence of the anionic detergent sodium dodecyl sulfate (SDS)

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Description

This quiz covers the essential and non-essential amino acids, their importance in nutrition, and their properties. It also touches on the pKa values of COOH and NH3.