Amino Acids and Proteins Overview

Questions and Answers

What is the role of the α carbon in amino acids?

It serves as a chiral center. (correct)

It determines the pKa values.

It is only found in nonpolar amino acids.

It is the main site for peptide bond formation.

Which of the following amino acid classes contains the most members?

Nonpolar, aliphatic (correct)

Polar, uncharged

Aromatic

Negatively charged

Which amino acid is unique for having a second hydrogen atom instead of an R group?

Cysteine

Glycine (correct)

Alanine

Serine

How many enantiomers can amino acids have?

Two Signup and view all the answers

The R group in amino acids is significant because it determines what?

The unique properties of each amino acid. Signup and view all the answers

Which of the following statements about L stereoisomers is true?

All amino acids in proteins are L stereoisomers. Signup and view all the answers

What are the four substituents attached to the α carbon in amino acids?

A carboxyl group, an amino group, a hydrogen atom, and an R group. Signup and view all the answers

Which class of amino acids is likely to be negatively charged at physiological pH?

Negatively charged Signup and view all the answers

How many amino acids belong to the aromatic class?

Three Signup and view all the answers

What is the primary structure of proteins characterized by?

Covalent bonds linking amino acid residues Signup and view all the answers

Which method uses cross-linked polyacrylamide gels to visualize proteins?

Electrophoresis Signup and view all the answers

Which technique is NOT typically used for studying protein structure at atomic resolution?

Cohen's D Signup and view all the answers

Which of the following describes the secondary structure of proteins?

Recurring structural patterns such as alpha helices and beta sheets Signup and view all the answers

What can mass spectrometry NOT determine about proteins?

Protein localization within a cell Signup and view all the answers

What does the purification factor in chromatography represent?

The ratio of final specific activity to starting specific activity Signup and view all the answers

What is the defining feature of oligomeric proteins?

Contain at least two identical subunits Signup and view all the answers

Which amino acid contributes the highest percentage in bovine cytochrome c?

Gly Signup and view all the answers

What is the primary purpose of 'salting out' in protein purification?

To selectively precipitate proteins based on solubility Signup and view all the answers

Which protein class contains a non-amino acid component known as a prosthetic group?

Conjugated proteins Signup and view all the answers

How is the number of amino acid residues in a protein estimated?

By dividing the molecular weight by 110 Signup and view all the answers

Which of the following is a characteristic of metalloproteins?

They contain specific metals Signup and view all the answers

What is the first step in the process of purifying proteins?

Breaking open cells to release proteins Signup and view all the answers

In column chromatography, what factor affects the migration rates of proteins through the solid phase?

The specific properties of the proteins Signup and view all the answers

What is the average molecular weight of an amino acid used for residue estimation?

~128 Signup and view all the answers

What defines a multisubunit protein?

Contains two or more polypeptides associated noncovalently Signup and view all the answers

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

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

Which R group type contributes to the hydrophobic effect in protein structures?

Nonpolar, aliphatic R groups Signup and view all the answers

Cysteine can participate in the formation of which type of bonds?

Disulfide bonds Signup and view all the answers

At a pH greater than the isoelectric point (pI), how does the amino acid’s net charge behave?

Net negative charge Signup and view all the answers

Which of the following describes the process of forming a peptide bond?

Formed through condensation of amino acids Signup and view all the answers

How many peptide bonds are found in a tripeptide?

2 Signup and view all the answers

Which of the following amino acid groups does NOT form hydrogen bonds?

Nonpolar, aliphatic R groups Signup and view all the answers

At what pH does a zwitterion of an amino acid occur?

pH = 7.0 Signup and view all the answers

Which of the following is true about protein molecular weight?

Polypeptides are more than 10 kDa Signup and view all the answers

Which notation indicates the sequence of amino acids in a peptide using one-letter codes?

AGT Signup and view all the answers

What principle does ion-exchange chromatography rely on for protein separation?

Net electric charge of the protein Signup and view all the answers

Which type of chromatography would be most effective for separating proteins based on their size?

Size-exclusion chromatography Signup and view all the answers

In ion-exchange chromatography, which factor can influence protein affinity?

The pH and concentration of free salt ions Signup and view all the answers

Which type of chromatography utilizes cation and anion exchangers?

Ion-exchange chromatography Signup and view all the answers

What will elute first from a gel filtration column?

Large proteins Signup and view all the answers

What can be used to elute proteins from affinity chromatography?

A high concentration of salt or ligand Signup and view all the answers

Considering a crude cellular extract with a total protein of 10,000 mg, which procedure would significantly reduce protein concentration?

Precipitation with ammonium sulfate Signup and view all the answers

What is the total activity after the precipitation with ammonium sulfate in the purification table?

32,000 units Signup and view all the answers

In the purification steps, what happens to specific activity as the sample size decreases?

It clearly increases Signup and view all the answers

What is the function of the bound charged groups in ion-exchange chromatography?

To attract specific proteins based on charge Signup and view all the answers

Study Notes

Amino Acids

Amino acids consist of an α carbon bonded to four substituents: a carboxyl group, an amino group, a hydrogen atom, and a unique R group (side chain).
Glycine is unique with a second hydrogen atom in place of an R group.
Amino acid residues in proteins are L stereoisomers, making them optically active.
Amino acids are classified into five main groups based on their R groups: nonpolar aliphatic, aromatic, polar uncharged, positively charged, and negatively charged.

pKa Values

Cysteine features three pKa values:
- pK1 for the carboxyl group: 1.96
- pK2 for the amino group: 10.28
- pK3 for its side chain: 8.18

Types of R Groups

Nonpolar, Aliphatic R Groups: Contribute to protein structure stability via the hydrophobic effect.
Aromatic R Groups: Absorb UV light at 270-280 nm and can enhance hydrophobic effects.
Polar, Uncharged R Groups: Capable of forming hydrogen bonds and disulfide bonds (e.g., cysteine).
Positively Charged R Groups: Display significant positive charge at physiological pH (7.0).
Negatively Charged R Groups: Carry a net negative charge at physiological pH (7.0).

Protonation States and Isoelectric Point (pI)

Amino acids can act as weak acids or bases; zwitterions dominate at neutral pH.
Titration reveals cation, zwitterion, and anion forms, with pK1 and pK2 defining acidic and basic characteristics, respectively.
For amino acids without ionizable side chains, pI is calculated as (pK1 + pK2) / 2.

Peptides

Peptides are chains of amino acids linked by covalent peptide bonds formed via condensation and cleaved by hydrolysis.
Types of peptides vary by the number of amino acids: dipeptide (2), tripeptide (3), oligopeptide (a few), polypeptide (many, <10 kDa), protein (thousands, >10 kDa).
Peptides are named from the amino-terminal (N-terminal) to the carboxyl-terminal (C-terminal) residue.

Peptide Composition and Subunits

Peptides can be multisubunit, formed from multiple polypeptides noncovalently, or oligomeric with identical subunits (protomers).

Protein Composition

Proteins have highly variable amino acid composition, exemplified by differences in bovine cytochrome c and chymotrypsinogen.

Estimation of Amino Acid Residues

The number of amino acid residues can be estimated as molecular weight/110, factoring out the water molecule lost during peptide bond formation.

Conjugated Proteins

Conjugated proteins contain non-amino acid components known as prosthetic groups, including lipids, carbohydrates, phosphate groups, heme, and specific metals.

Protein Separation and Purification

Proteins can be separated based on size, charge, binding properties, and solubility. Common methods include salt precipitation, fractionation, dialysis, and chromatography.

Column Chromatography

Protein migration utilizes a buffered solution through a solid phase, with the rate affected by protein properties.

Electrophoresis

Utilized to visualize and analyze purified proteins based on charge-to-mass ratios. Involves polyacrylamide gels and staining methods for visualization.

Protein Structure Levels

Four structural levels:
- Primary: Linear sequence and covalent bonds of amino acids.
- Secondary: Patterns like alpha-helices and beta-sheets.
- Tertiary: 3D folding configuration.
- Quaternary: Assembly of multiple polypeptide chains.

Protein Structural Analysis Techniques

Traditional protein sequencing methods involve protein labeling and protease digestion.
Advanced techniques include X-ray crystallography, NMR spectroscopy, and Cryo-EM for atomic resolution structure.
Mass spectrometry offers insights into molecular mass, amino acid sequences, and proteomes.

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Description

This quiz covers the structural features of amino acids, including the α carbon and its four substituents. Dive into the unique characteristics of various amino acids and their role in forming peptides and proteins. Ideal for students studying biochemistry or molecular biology.