BCH3004 Amino Acids Quiz
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Questions and Answers

Explain why glycine is the only amino acid that does not contain a chiral carbon.

Glycine has two hydrogen atoms attached to its α-carbon, making it achiral. All other amino acids have four different substituents attached to their α-carbon, making them chiral.

Why is the formation of a peptide bond considered a condensation reaction?

A peptide bond forms when a water molecule is eliminated from the α-carboxyl group of one amino acid and the α-amino group of another amino acid.

Describe the difference between an amino acid and an amino acid residue.

An amino acid is the individual monomer unit, while an amino acid residue is the portion of that amino acid that remains after it has been incorporated into a peptide chain.

How are the L and D forms of amino acids related to each other?

<p>They are nonsuperimposable mirror images of each other, meaning they are enantiomers.</p> Signup and view all the answers

What is the significance of the N-terminal and C-terminal ends of a peptide chain?

<p>The N-terminal end has a free amino group, while the C-terminal end has a free carboxyl group. This directionality is important for protein synthesis and function.</p> Signup and view all the answers

Explain why polypeptides are considered metastable.

<p>Polypeptides are susceptible to hydrolysis. They can break down into their individual amino acids under extreme conditions or in the presence of catalysts.</p> Signup and view all the answers

What is the significance of the beta carbon (Cβ) in the context of amino acid structure?

<p>While not directly involved in peptide bond formation, the beta carbon can be a site of additional stereocenters, such as in isoleucine and threonine.</p> Signup and view all the answers

How does the formation of a peptide bond differ from the formation of other types of covalent bonds?

<p>The peptide bond involves the specific interaction between the carboxyl group of one amino acid and the amino group of another, resulting in the release of a water molecule.</p> Signup and view all the answers

What is the difference between a dipeptide and a polypeptide?

<p>A dipeptide consists of two amino acids linked by a peptide bond, while a polypeptide contains a chain of multiple amino acids linked by peptide bonds.</p> Signup and view all the answers

Why is the suffix –yl used to replace –ine or –ate in the name of an amino acid residue?

<p>It emphasizes that the amino acid is part of a peptide chain and not its individual free form.</p> Signup and view all the answers

Explain the significance of aromatic amino acids in protein analysis, highlighting their unique property.

<p>Aromatic amino acids, such as phenylalanine, tyrosine, and tryptophan, absorb light in the near ultraviolet region of the electromagnetic spectrum. This property is used for protein detection and quantification by measuring their absorption at 280 nm.</p> Signup and view all the answers

Describe the process of titration as it applies to amino acids, focusing on the reaction involved.

<p>Titration of amino acids involves the reaction of each functional group, such as the amino group (NH2) and the carboxyl group (COOH), with a hydrogen ion (H+). This reaction changes the charge of the functional group, affecting the overall charge of the amino acid.</p> Signup and view all the answers

What is the isoelectric point (pI) of an amino acid, and how is it determined for an amino acid with two ionizable groups?

<p>The isoelectric point (pI) is the pH at which a molecule has no net charge. For an amino acid with two ionizable groups, the pI is calculated as the average of the pKa values of the two groups: pI = (pKa1 + pKa2) / 2.</p> Signup and view all the answers

Explain the concept of 'polyampholytes' as it relates to proteins, and provide an example.

<p>Proteins are considered polyampholytes because they contain multiple acidic and basic groups. This results in a net charge that can vary depending on the pH of the environment. For example, human hemoglobin, with its 148 ionizable groups, has a pI of 6.85.</p> Signup and view all the answers

Describe the significance of the isoelectric point (pI) in protein separation techniques, illustrating with an example.

<p>The isoelectric point (pI) is crucial in protein separation methods like electrophoresis and isoelectric focusing. Proteins migrate differently in an electric field based on their charge. At their pI, proteins have no net charge and will not migrate.</p> Signup and view all the answers

Briefly explain the principle behind two-dimensional electrophoresis and its application in protein separation.

<p>Two-dimensional electrophoresis separates proteins based on two properties: their isoelectric point (pI) and their molecular weight. The first dimension separates proteins based on their pI using isoelectric focusing. The second dimension separates proteins based on their molecular weight using SDS-PAGE, resulting in a complex, two-dimensional map of proteins.</p> Signup and view all the answers

Compare and contrast the roles of selenocysteine and pyrrolysine as rare genetically encoded amino acids.

<p>Both selenocysteine (Sec) and pyrrolysine (Pyl) are rare amino acids, expanding the genetic code beyond the standard 20. Selenocysteine is widely distributed but found in fewer proteins. Its role often involves redox reactions. Pyrrolysine, found predominantly in archaea and eubacteria, is involved in the formation of specific enzymes.</p> Signup and view all the answers

Explain how the charge of an amino acid changes with the pH of the environment.

<p>Amino acids have functional groups that can either gain or lose protons (H+), affecting their charge. At low pH (acidic), the amino group (NH2) is protonated to become NH3+, while the carboxyl group (COOH) remains protonated. As the pH increases (becomes more basic), the carboxyl group deprotonates to COO-.</p> Signup and view all the answers

Explain how the location of a positively charged amino acid influences its role in protein structure and function.

<p>Positively charged amino acids located on the exterior surfaces of proteins can interact with water molecules in the aqueous environment, contributing to protein solubility. They can also participate in substrate binding in enzyme active sites.</p> Signup and view all the answers

What is the significance of the ionization of histidine's side chain in biological systems, and how is it related to the isoelectric point?

<p>Histidine has a titratable side chain that can be either protonated or deprotonated, depending on the pH. This ionization plays a crucial role in enzyme catalysis and protein-protein interactions. Its pKa value is close to physiological pH, making it important for regulating the charge of proteins and influencing their function.</p> Signup and view all the answers

What is the significance of the 'alpha' designation in alpha-amino acids?

<p>The 'alpha' designation indicates that the amino group is attached to the alpha-carbon, which is the carbon adjacent to the carboxylic acid group.</p> Signup and view all the answers

How do amino acids exist at near natural pH?

<p>At near natural pH, amino groups are protonated (-NH3+) and carboxylic acid groups are deprotonated (COO-), resulting in the zwitterion form.</p> Signup and view all the answers

What are the characteristics of nonpolar (hydrophobic) amino acids?

<p>Nonpolar amino acids are hydrophobic and typically found in the interior of protein structures, avoiding contact with water.</p> Signup and view all the answers

Identify the roles of polar uncharged amino acids in proteins.

<p>Polar uncharged amino acids stabilize protein structures through hydrogen bonding and are often exposed on protein surfaces.</p> Signup and view all the answers

Explain the significance of acidic amino acids at physiological pH.

<p>Acidic amino acids carry negative charges at physiological pH, making them hydrophilic and often located on the protein's surface.</p> Signup and view all the answers

What distinguishes selenocysteine and pyrrolysine from standard amino acids?

<p>Selenocysteine and pyrrolysine are incorporated into proteins but are found in only a small number of them, unlike the standard 20 amino acids.</p> Signup and view all the answers

How do structural features of proline differ from other amino acids?

<p>Proline is classified as an imino acid due to its unique cyclic structure, where the amino group is bonded to the side chain.</p> Signup and view all the answers

What type of chemical reaction do cysteine residues undergo?

<p>Cysteine residues can undergo oxidation to form disulfide bridges (-S-S-) between thiol groups, stabilizing protein structure.</p> Signup and view all the answers

Describe the optical activity of amino acids.

<p>Amino acids are optically active due to the presence of a chiral alpha-carbon, which results in two enantiomers that are mirror images.</p> Signup and view all the answers

What is the primary function of the side chain (R group) in amino acids?

<p>The side chain (R group) determines the characteristics of the amino acid, influencing its interactions and role within proteins.</p> Signup and view all the answers

Flashcards

Chiral Carbon

A carbon atom bonded to four different substituent groups.

Stereoisomer

A molecule with a chiral carbon that has two possible, non-superimposable mirror images.

Enantiomers

Two stereoisomers that are mirror images of each other.

L-form Amino Acids

The most common spatial arrangement of amino acids found in nature.

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Peptide Bond

A covalent bond formed between the α-carboxyl group of one amino acid and the α-amino group of another amino acid.

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Dipeptide

A molecule formed by joining two amino acids together with a peptide bond.

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Polypeptide

A peptide chain with multiple amino acid residues joined by peptide bonds.

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N-terminal

The end of a peptide chain that has a free amino group.

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C-terminal

The end of a peptide chain that has a free carboxyl group.

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Hydrolysis

The process of breaking down a peptide chain into individual amino acids by adding water.

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What are proteins made of?

Proteins are large molecules composed of smaller building blocks known as amino acids, connected in a chain.

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Why are amino acids called α-amino acids?

The α-carbon is the carbon atom next to the carboxyl group in an amino acid. The amino group is directly attached to this α-carbon.

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What is the general structure of an amino acid?

All amino acids share a common structure: a central carbon (α-carbon) attached to a carboxyl group, an amino group, a hydrogen atom, and a unique side chain (R group).

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What makes amino acids different from each other?

The unique side chain (R group) differentiates one amino acid from another, giving each amino acid its specific properties.

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How do amino acids exist at neutral pH?

At physiological pH (near 7), the carboxyl group loses a proton (H+) becoming negatively charged (COO-) and the amino group gains a proton becoming positively charged (-NH3+).

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What is a zwitterion?

A zwitterion is an amino acid with both a positive and a negative charge, existing in a neutral state.

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What are hydrophobic amino acids?

Hydrophobic amino acids have nonpolar side chains (R groups) that tend to avoid water and cluster together in the interior of proteins.

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What are hydrophilic amino acids?

Hydrophilic amino acids have polar side chains (R groups) that are attracted to water and are often found on the surface of proteins.

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How are amino acids classified?

Amino acids can be classified based on the properties of their side chains (R groups). These properties influence the structure and function of proteins.

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What is the significance of the 20 common amino acids?

The 20 amino acids commonly found in proteins play important roles in the structure, function, and regulation of biological processes.

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Positively Charged Amino Acids

Amino acids with a positively charged side chain at or near neutral pH. They are often found on the exterior surfaces of proteins, where they can be hydrated by the aqueous environment or in the substrate binding cleft of an enzyme.

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Aromatic Amino Acids

Amino acids that absorb light in the near ultraviolet (UV) region of the electromagnetic spectrum. This property allows for the detection and quantification of proteins by measuring their absorbance at 280 nm.

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Rare Genetically Encoded Amino Acids

Selenocysteine (Sec) is the 21st amino acid and pyrrolysine (Pyl) is the 22nd amino acid. These amino acids are less common than the standard 20, but they play important roles in certain proteins.

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Titration of Amino Acids

The process of reacting each functional group of an amino acid with a hydrogen ion. This reaction helps to determine the ionization state of the amino acid.

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Isoelectric Point (pI)

The pH at which a molecule has no net charge. At its isoelectric pH, a molecule will not migrate in an electric field.

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Calculating Isoelectric Point (pI)

The isoelectric point (pI) of an amino acid is determined by the pKa values of its ionizable groups.

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Isoelectric Point (pI) of Proteins

Proteins have many acidic and basic groups, making them polyampholytes. They have an isoelectric point (pI), where the net charge is zero.

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Isoelectric Focusing

A technique that separates proteins based on their isoelectric point.

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Two-Dimensional Electrophoresis

A technique that separates proteins based on both their isoelectric point and their molecular weight.

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Study Notes

BCH3004 Principles in Biochemistry

  • Course code: BCH3004
  • Course title: Principles in Biochemistry
  • Course credit: 4(3+1)
  • Lecturer: TS. Dr. Azzreena Mohamad Azzeeme
  • Department: Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, UPM

Amino Acids

  • Amino acids are the building blocks of proteins
  • Properties, structure, and function
  • Classification of amino acids
  • Chemical reactions
  • Optical activity
  • Chirality
  • Unique amino acids

Learning Outcomes

  • Students can explain the properties, structure, function, and classification of amino acids.
  • Students can explain chemical reaction, optical, and chirality activity of amino acids.

Structure of Amino Acids

  • Proteins are polymers composed of amino acids
  • Amino acids are monomers
  • α-amino acids: The amino group is attached to the α-carbon, which is the carbon atom adjacent to the carboxyl group.

Structure of Amino Acids (Continued)

  • Amino acids have a central α-carbon atom
  • Amino group (-NH3+)
  • Carboxyl group (-COO-)
  • Side chain (R group)

Properties of Common Amino Acids

  • Table 5.1 details properties of common amino acids (e.g., abbreviations, pKa, mass)

Near Natural pH

  • Carboxyl group is deprotonated (COO-)
  • Amino group is protonated (-NH3+)
  • Zwitterion form

Common Amino Acids

  • 20 amino acids are commonly incorporated in proteins during translation
  • Some rare amino acids, selenocysteine and pyrrolysine, are also found

Aromatic Amino Acids

  • Absorb light in the near ultraviolet region of the electromagnetic spectrum
  • Used for detection and/or quantification of proteins by measuring absorption at 280 nm

Rare Genetically Encoded Amino Acids

  • Selenocysteine (Sec)
  • Pyrrolysine (Pyl)

Titration of Amino Acids

  • Amino acids have cationic, neutral (zwitterion), and anionic forms depending on pH.

Isoelectric pH (pI)

  • Point where average charge of an amino acid is zero
  • pI is used in separation methods
  • Formula varies depending on the number of ionizable groups

Proteins and Polyampholytes

  • Proteins contain many acidic and/or basic groups
  • Called polyampholytes
  • Tens of hundreds of individual groups
  • Isoelectric pH of protein is dependent on its constituent amino acids
  • Determined experimentally using techniques like electrophoresis and isoelectric focusing

Two-Dimensional Electrophoresis

  • Separates proteins based on isoelectric point and molecular weight.

Exercise 1

  • Glutamic acid and lysine structures

Stereochemistry of α-Amino Acids

  • Chiral carbon: Four different substituents attached
  • Stereocenter
  • Molecules with one asymmetric carbon have two stereoisomers (e.g., L and D forms).

Stereoisomers of α-amino acids

  • Non-superimposable mirror images
  • L and D forms
  • All amino acids, except glycine, have an asymmetric α-carbon.
  • Isoleucine and threonine also have a chiral β-carbon.

Peptides and Peptide Bond

  • Individual amino acids linked by peptide bonds
  • Formed by the removal of water (condensation reaction)
  • Bond formation between α-carboxyl group of one amino acid and α-amino group of the next

Direction of Peptide Chain

  • N-terminal to C-terminal
  • Amino acid residues (portion of amino acid remaining in the chain)
  • Suffix -yl is used in amino acid residue names.

Biological Functions of Small Peptides

  • Oxytocin
  • Vasopressin

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BCH3004 Principles In Biochemistry - Amino Acids PDF

Description

Test your knowledge on amino acids with this quiz from the Principles in Biochemistry course. Evaluate your understanding of their properties, structure, function, and classification, as well as their chemical reactions and chirality. Perfect for students looking to reinforce their biochemistry knowledge.

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