BIOC 192 Lecture 4: Amino Acids & Peptides

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Questions and Answers

What is the main function of the side chains in amino acids?

To regulate protein synthesis

To provide amino acids with their unique properties (correct)

To facilitate energy production

To determine the amino acid's role in metabolism

All amino acids have the same side chains.

False

What term describes the covalent bond formed between amino acids?

peptide bond

The twenty amino acids can be represented by a full name, a 3-letter name, and a ______ name.

1-letter Signup and view all the answers

Match the following types of bonds with their characteristics:

Peptide bond = Links amino acids together in proteins Ionic bond = Forms between charged side chains Hydrogen bond = Stabilizes secondary structure of proteins Disulfide bond = Links cysteine residues in proteins Signup and view all the answers

Which property of amino acids is primarily responsible for their function in proteins?

The variety of side chains Signup and view all the answers

Amino acids exist as zwitterions only in solid form.

False Signup and view all the answers

How many amino acids are commonly known?

twenty Signup and view all the answers

Which of the following modifications is essential for blood clotting?

Carboxylation Signup and view all the answers

Cysteine can form a peptide bond with another cysteine.

False Signup and view all the answers

What is the term for modifications that occur to amino acids after they are added to a protein?

post-translational modification Signup and view all the answers

A covalent bond that links amino acids together is called a ______.

peptide bond Signup and view all the answers

Which amino acid is often involved in hydroxylation?

Proline Signup and view all the answers

Match the type of amino acid modification to its function:

Phosphorylation = Controls enzyme activity Hydroxylation = Prevents connective tissue diseases Carboxylation = Necessary for blood clotting Glycosylation = Involves sugar addition Signup and view all the answers

All amino acids start out as one of the standard 20.

True Signup and view all the answers

Who determined the structure of the peptide bond through X-ray crystallography in the 1930s-1940s?

Linus Pauling and Robert Corey Signup and view all the answers

What type of side chains do negatively charged amino acids have?

Polar side chains Signup and view all the answers

All amino acids are chiral.

False Signup and view all the answers

What are the one-letter and three-letter abbreviations for Glycine?

G and Gly Signup and view all the answers

The pI, or isoelectric point, is the pH at which an amino acid has a net charge of _____ .

zero Signup and view all the answers

Match each amino acid to its special characteristic:

Glycine = Non-chiral Proline = Imino acid Lysine = Positively charged Aspartate = Negatively charged Signup and view all the answers

Which amino acid is characterized by the presence of an imino group?

Proline Signup and view all the answers

One-letter abbreviations for amino acids are primarily used for sequence alignment.

True Signup and view all the answers

What is the pKa value in relation to an ionisable group on an amino acid?

The pH at which the group is 50% ionised. Signup and view all the answers

The mutation from glutamate to valine at position 6 is denoted as _____ .

E6V Signup and view all the answers

Which of the following amino acids is classified as basic?

Lysine Signup and view all the answers

What is a peptide primarily made of?

Amino acids Signup and view all the answers

A peptide bond primarily exists in a cis configuration.

False Signup and view all the answers

What term is used for amino acids once they are linked in a peptide or protein?

Amino acid residues Signup and view all the answers

The peptide bond that links amino acids has a rotational barrier of approximately _______ kJ/mol.

80 Signup and view all the answers

What do we mean when we say amino acids are chiral?

They have an asymmetric carbon atom. Signup and view all the answers

Match the following terms with their definitions:

pKa = The acid dissociation constant pI = The isoelectric point Post-translational modifications = Chemical changes after protein synthesis Amino acid side chains = Functional groups attached to the backbone Signup and view all the answers

What are the 4 main groups of amino acids?

Non-polar, Polar, Charged, Ionizable Signup and view all the answers

One common example of a post-translational modification is _______.

phosphorylation Signup and view all the answers

Which amino acids are predominantly used in the synthesis of proteins in living organisms?

L-amino acids Signup and view all the answers

All amino acids have polar side chains.

False Signup and view all the answers

What is the central atom in an amino acid to which the amino group, carboxyl group, and side chain are attached?

Alpha carbon Signup and view all the answers

Amino acids can exist in both D- and L- forms due to the presence of a point of __________.

asymmetry Signup and view all the answers

Match the following classifications of amino acids with their characteristics:

Non-polar = Have aliphatic carbon or aromatic ring side chains Polar = Contain ionizable acidic or basic groups Basic = Positively charged at physiological pH Acidic = Negatively charged at physiological pH Signup and view all the answers

Which of the following defines the importance of the peptide bond?

It links amino acids together in a stable manner Signup and view all the answers

How do amino acids generally differ from each other?

In their R-group side-chain chemical structure Signup and view all the answers

The structure of the peptide bond is rigid and allows for free rotation between adjacent amino acids.

False Signup and view all the answers

At pH 7, aspartate and glutamate primarily exist in which form?

Ionic form Signup and view all the answers

The isoelectric point (pI) is the pH at which a protein has a net charge of zero.

True Signup and view all the answers

What is the pKa range of α-amino groups in amino acids?

9-10 Signup and view all the answers

Cysteine contains a __________ group that can form disulfide bonds.

thiol Signup and view all the answers

Match the amino acid to its classification based on charge at pH 7:

Lysine = Basic Aspartate = Negative Arginine = Basic Glutamate = Negative Signup and view all the answers

Which of the following amino acids has an ionizable side chain?

Lysine Signup and view all the answers

All amino acids contain at least one acidic and one basic group.

False Signup and view all the answers

Name one amino acid that appears frequently in the active sites of enzymes due to its ionizable side chain.

Histidine Signup and view all the answers

Which of the following is a type of post-translational modification?

Proteolytic cleavage Signup and view all the answers

All post-translational modifications enhance the function of proteins.

False Signup and view all the answers

What type of modification is known to facilitate the formation of disulfide bridges in proteins?

Cysteine Signup and view all the answers

One common post-translational modification that involves the addition of a sugar molecule is called _____ -glycosylation.

N Signup and view all the answers

Match the following modifications to their examples:

N-glycosylation = Addition of sugar Hydroxylation = Collagen Phosphorylation = Milk proteins C-terminal amidation = Bioactive peptides Signup and view all the answers

What does the pKa value indicate about an ionisable group in an amino acid?

The pH at which 50% of the group is ionised Signup and view all the answers

The peptide bond primarily exists in a cis configuration.

False Signup and view all the answers

What is the term for the first amino acid in a protein chain?

N-terminus Signup and view all the answers

The sequence of amino acids in a protein is known as the ______ sequence.

primary Signup and view all the answers

Match the following terms with their corresponding descriptions:

Peptide bond = Covalent bond linking amino acids N-terminus = The start of an amino acid chain C-terminus = The end of an amino acid chain Trans configuration = Functional groups on opposite sides Signup and view all the answers

Which statement correctly describes the characteristics of peptide bonds?

Peptide bonds have double bond character due to electron resonance. Signup and view all the answers

Amino acids are always neutral at the isoelectric point (pI).

True Signup and view all the answers

What defines the function and structure of a mature protein?

The linear sequence of amino acids Signup and view all the answers

Study Notes

Learning Objectives

Understand amino acid properties and their relevance to protein structure and function.
Identify types of amino acid side chains and their chemical properties.
Comprehend the formation of peptides and proteins from amino acids.
Recognize the importance and structure of the peptide bond.

Amino Acids Overview

There are twenty standard amino acids, each with a common backbone but different side chains.
Amino acids have full names, three-letter abbreviations, and one-letter codes.
Amino acid side chains are responsible for the biochemical activity of proteins.

Amino Acid Classification

Amino acids can be categorized based on the chemical properties of their side chains, including:
- Nonpolar (hydrophobic)
- Polar (hydrophilic)
- Positively charged (basic)
- Negatively charged (acidic)

Amino Acid Specificities

Glycine (G) is non-chiral and provides flexibility; it is unique among amino acids.
Proline forms a rigid structure due to bonding back to its main chain.

Ionization and Charges

Amino acids in solution exist as zwitterions, having both positive and negative charges.
Some amino acids possess ionizable side chains; their charge depends on pH and is described by pKa values.
pI (isoelectric point) is the pH where an amino acid has no net charge.

Amino Acid Modifications

Standard amino acids can undergo post-translational modifications after translation, including:
- Phosphorylation: regulates enzyme activity.
- Hydroxylation: critical for collagen formation and preventing scurvy.
- Carboxylation: important for blood clotting.
- Other modifications include glycosylation, iodination, and metal binding.

Peptide Bonds

Peptide bonds link amino acids via a covalent bond formed between the carboxyl group of one amino acid and the amino group of another.
The peptide bond exhibits about 40% double bond character, leading to a planar and predominantly trans configuration.
Peptide chains vary in length and have biological functions; short chains are called peptides, while longer chains are proteins.
Each amino acid linked in a chain is termed an amino acid residue, denoted by its sequence position (e.g., Met 184).

Summary of Key Terms

pKa: The pH at which an ionizable group is 50% ionized.
pI: The pH at which an amino acid or protein has a net charge of zero.
Amino acid modifications are crucial for protein functionality and regulation.

Building Blocks of Proteins: Amino Acids

Amino acids are the fundamental units of proteins, containing both an amino group (H2N–) and a carboxyl group (–COOH), linked to a central α-carbon atom.
There are 20 standard amino acids in proteins, classified based on their side-chain structures (R-groups).
Amino acids exhibit stereochemistry with D- and L- forms; proteins in living organisms primarily utilize L-amino acids.
Bacteria can synthesize proteins containing D-amino acids.

Classification of Amino Acids

Amino acids are categorized into non-polar (aliphatic or aromatic side chains) and polar (ionizable acidic or basic groups) types.
Non-polar amino acids are typically found in hydrophobic environments, while polar amino acids interact with the aqueous environment.
Ionizable side chains contribute to the overall charge of the amino acid, influenced by pH and pKa values.

Peptide Bonds Formation

Amino acids join by peptide bonds, forming a covalent linkage between the amino (N-terminus) and carboxyl (C-terminus) ends of adjacent amino acids.
The peptide bond has partial double bond character, making it planar and predominantly in trans configuration.
The sequence of amino acids, or primary structure, is written from N-terminus to C-terminus and defines the protein's structure and function.

Peptide Bond and Protein Structure

The peptide bond is stable and contributes to the protein's final three-dimensional structure through its fixed dipole.
The role of cis/trans configurations in peptide bonds is essential, with cis indicating similar sides and trans indicating opposite sides of the carbon chain.

Post-Translational Modifications

Proteins undergo post-translational modifications, enhancing functionality after translation from the endoplasmic reticulum through the Golgi apparatus.
Common modifications include:
- Proteolytic cleavage
- N-glycosylation
- Lipid addition
- Disulphide bridge formation
- Hydroxylation
- C-terminal amidation
- Phosphorylation
These modifications are crucial for achieving the correct active form of proteins.

Protein Functionality

The ultimate function of proteins is determined by the amino acid sequence, structural conformation, and post-translational modifications.
Proteins perform various roles, including:
- Enzymatic activity
- Regulatory functions
- Transport mechanisms
- Storage solutions
- Contractile and motility functions
- Structural frameworks
- Protective roles in the body

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Description

Dive into the building blocks of proteins with Lecture 4 of BIOC 192. This session focuses on amino acids, peptides, and the interplay of the peptide bond, providing a foundational understanding crucial for biochemistry students. Engage with the material to enhance your knowledge of protein structure and function.