Biochemistry: Amino Acids and Peptides

Podcast

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What type of reaction forms a peptide bond between two amino acids?

Oxidation reaction

Hydrolysis reaction

Redox reaction

Condensation reaction (correct)

Which amino acid is part of the dipeptide alanylserine?

Glutamate

Asparagine

Serine (correct)

Leucine

At physiological pH (approximately 7), what is the value of [H+]?

$10^{-8} M$

$10^{-7} M$ (correct)

$10^{-9} M$

$10^{-6} M$

Which groups in amino acids can act as acids and bases?

Amine and α-carboxylate groups Signup and view all the answers

What does the Henderson-Hasselbalch equation relate?

pH, pKa, and the state of ionization Signup and view all the answers

Which of the following best describes the physiological pH range?

7.0 - 7.4 Signup and view all the answers

What happens to amino acid groups when the availability of H+ in solution changes?

They can gain or lose protons Signup and view all the answers

Which of these structural components is involved in forming a dipeptide?

α-carboxyl group and α-amino group Signup and view all the answers

What configuration do amino acids in proteins predominantly have?

L configuration Signup and view all the answers

What is the process of forming peptide bonds between amino acids called?

Condensation Signup and view all the answers

What is the average molecular weight of an amino acid residue in a protein, after accounting for the water removed during peptide bond formation?

128 – 18 = 110 Da Signup and view all the answers

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

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

What type of amino acids includes those with very non-polar side chains?

Aliphatic amino acids Signup and view all the answers

Which property is NOT associated with the amino acids with negatively charged side chains?

Basic in nature Signup and view all the answers

Which amino acid side chains are categorized as having polar but uncharged structures?

Hydroxyl-containing amino acids Signup and view all the answers

What is the common backbone of all amino acids primarily made of?

Carbon, hydrogen, and nitrogen Signup and view all the answers

What characterizes an oligopeptide?

Composed of a few amino acids and usually a fragment Signup and view all the answers

What is the main function of the C=O group in the formation of peptide bonds?

Weakens the bond for water attack Signup and view all the answers

What happens to tightly bound amino acids as the concentration of Na+ increases?

They are progressively displaced. Signup and view all the answers

Which of the following correctly describes a method for identifying amino acids in a mixture?

Through their elution volumes compared to common standards. Signup and view all the answers

What is primarily used to separate proteins based on charge differences during ion exchange chromatography?

The relative number of positive and negative amino acids. Signup and view all the answers

Why might pH be adjusted during the ion exchange process?

To eliminate the positive charge on amino acids. Signup and view all the answers

Approximately what percentage of proteins are negatively charged at pH 7?

65% Signup and view all the answers

What happens to the three functional groups of glutamic acid as pH increases from 0 to 14?

Each group becomes deprotonated at different pH levels. Signup and view all the answers

At what pH value is 50% of a functional group in the protonated form when it is equal to its pKa?

pH is equal to the pKa. Signup and view all the answers

Which statement accurately reflects the behavior of ionizable groups in amino acids?

The pKa value can vary depending on the chemical context. Signup and view all the answers

What occurs to the ionization of glutamic acid when pH is approximately 1 unit below its pKa?

All groups are in their protonated form. Signup and view all the answers

Why might the pKa of an amino acid differ in a peptide chain compared to its free form?

Interactions with neighboring amino acids affect its environment. Signup and view all the answers

What factor primarily determines whether a protein can enter the pores during gel filtration?

Size of the protein Signup and view all the answers

In gel filtration chromatography, which proteins elute first?

Larger proteins Signup and view all the answers

Which method can be used to determine the molar mass of an unknown protein?

Comparing the elution volume to known proteins Signup and view all the answers

What linear relationship is observed in the elution volume when measuring molar mass in gel filtration?

Elution volume has a negative slope with respect to log molar mass Signup and view all the answers

What is the primary purpose of electrophoresis in studying proteins?

To visualize and characterize purified proteins Signup and view all the answers

Which parameter does NOT affect the rate of movement during electrophoresis?

Concentration of buffer Signup and view all the answers

Which material is used to prepare gels for electrophoresis?

Polyacrylamide Signup and view all the answers

What range of protein sizes is polyacrylamide gel particularly suitable for during electrophoresis?

10 kDa - 1000 kDa Signup and view all the answers

What can be estimated from the electrophoresis of a protein mixture?

Degree of purity of a mixture Signup and view all the answers

Why is Coomassie blue dye used in protein studies?

To bind to proteins for visualization Signup and view all the answers

Study Notes

L and D Isomers

L-Alanine and D-Alanine are mirror images of each other
Amino acids found in proteins are in the L configuration

Peptide Bonds

Peptide bond formation involves removal of H2O
Breaking a peptide bond regenerates the original carboxylic acid and amino group
The C=O group of the amide is vulnerable to attack by H2O

Peptide Chains

A combination of different side chains (R1, R2, R3, etc.) gives each protein unique properties
Myoglobin has 153 amino acids (16.5 kDa)
Polypeptide - A chain with many amino acids, usually a complete protein
Oligopeptide - A chain with a few amino acids, usually a fragment

Amino Acid Residues & Molecular Weight

Amino acids in a protein chain are known as amino acid residues because water is removed when peptide bonds are formed
The average molecular weight of amino acids in proteins is ~128
The average molecular weight of an amino acid residue in a protein is 110 (128 - 18)
The number of amino acid residues in a protein can be estimated by dividing the molecular weight of the protein by 110

Amino Acid Side Chain Structure

Carbon atoms of the amino acid core are identified by Greek letters
The alpha carbon is the central backbone atom
The beta carbon is the first atom of the side chain
Functional groups can be linked to different core atoms, including:
- alpha-amino
- epsilon-amino

The 20 Natural Amino Acids

Amino acids share a common backbone, but differ in their side chains
You need to be able to recognize the structures of the amino acids and know their 1 and 3 letter codes
You need to be able to associate specific properties with each amino acid:
- Hydrophobicity
- Charge
- Special chemical reactivity
Amino acids are grouped according to their structures or by their similar properties

Amino Acid Groupings

6 with very non-polar side chains
5 with moderately non-polar side chains
4 with polar but uncharged side chains
3 with positively charged side chains (very polar)
2 with negatively charged side chains (very polar)

Amino Acid Quiz

Try to identify as many amino acids as possible.
Asp (D) - Aspartate
Glu (E) - Glutamate

Homework Questions (Answer for Question # 1)

Join Ala and Ser together through a peptide bond to form the dipeptide alanylserine (Ala-Ser)
Answer:
- H O H
- H3N+ C C N C COO-
- CH3 H CH2
- OH

Alanylserine: The Condensation Reaction

H O H
H3N+ C C OH :N C COO-
CH3 H CH2
OH
H2O
H O H
H3N+ C C N C COO-
CH3 H CH2
OH

Amino Acids as Acids and Bases

The alpha amino and alpha carboxylate groups of amino acids, as well as the side chains of certain amino acids can act as acids and bases
These groups will gain (protonate) or lose (deprotonate) H+ depending on the availability of H+ in the solution
Normal biochemical processes occur close to pH 7 (physiological pH is 7.0 - 7.4)
pH is an expression of available H+ : pH = - log10[H+]
- At pH=7, [H+]=10-7 M
The Henderson-Hasselbalch Equation relates pH, pKa, and the state of ionization of a given group

The Ionization State of the Alpha-Carboxylate Group at pH 7 (Glutamate)

A molecule can have several ionizable groups
Each group has its own pKa value
The pKa value depends on its chemical context
An amino acid will have a slightly different pKa when it is part of a peptide chain, for example:
- Alpha-amino pKa = 9.5
- Alpha-carboxylate pKa = 2.1
- Gamma-carboxylate pKa = 4.1

Ionization of Glutamic Acid as pH Increases

Starting with glutamic acid at a very low pH, all three functional groups are fully protonated
As pH is raised, [H+] becomes less available, so deprotonation is more likely
Each group undergoes a transition as pH shifts from 0-14, starting ~1 unit below its pKa and almost complete by ~1 unit above its pKa
When pH = pKa, 50% of the group is in the protonated form, and 50% is in the deprotonated form
Once a group deprotonates, it remains that way for the rest of the pH range

The Ionization State of a Group at a Given pH

The ionization state of a group at a given pH depends on its pKa value

Separation of Amino Acids by Ion Exchange Chromatography

Amino acids are detected and their concentrations are measured in the buffer coming out of the column
Elution volume is the volume of buffer needed to move a given amino acid from the top to the bottom of the column
Elution volumes are characteristic for each amino acid, and are often compared to a common standard such as Ala or Leu
Elution volumes allow amino acids to be identified

Separation of Proteins from Complex Mixtures

Proteins are derived from natural sources, such as:
- Microbial cultures
- Plants
- Animal tissues like liver
Cells are broken open to release the proteins into a solution - extract
Extracts may contain thousands of different proteins
Separation by ion exchange is based on charge differences among proteins:
- Depends on the relative number of Asp + Glu (negative) versus His + Lys + Arg (positive) in each protein, and on pH
- ~65% of all proteins are negatively charged at pH 7

Charge Differences Among Peptides and Proteins

Size Exclusion Chromatography relies on size differences of proteins:
- Protein molecules can enter pores if they fit
- Larger proteins are excluded from pores
- Proteins of intermediate size may enter some of the pores
Proteins separate by size, larger proteins elute first, and and smaller proteins elute later

Molar Mass Measurement by Gel Filtration

Gel Filtration can be used to measure the molar mass of proteins by comparing a sample to proteins of known size
Measures Ve (elution volume), which is the volume of buffer needed to move protein from the top to the bottom of the column
Ve is a linear function of log molar mass (negative slope)

Protein Separation and Characterization by Electrophoresis

Electrophoresis - Movement of charged molecules in an electric field
Does not contribute to purification as structure is commonly affected by electrophoresis
Can visualize and characterize purified proteins
Can be used to estimate:
- Number of different proteins in a mixture
- Degree of purity of a mixture
- Isolectric point
- Approximate molecular weight
Rate of movement depends on size, shape, and charge

Polyacrylamide Gel Electrophoresis

Polyacrylamide gel is easily prepared in the lab and has the right porosity for proteins 10kDa - 1000kDa
Electrophoresis of proteins is generally carried out in gels made up of the polymer polyacrylamide
A typical gel is 5-15% polymer and 90-95% water with conductive buffer
Separated proteins are visualized by adding a dye such as Coomassie blue which binds to proteins

Studying That Suits You

Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

Description

Explore the intricate world of amino acids and peptides in this quiz. Learn about L and D isomers, peptide bond formation, and the unique properties of polypeptide chains. Test your knowledge of molecular weights and amino acid residues in proteins.