Biochemistry I PHBC 522 Lecture 1

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Questions and Answers

What is the significance of posttranslational modifications of amino acid side chains in proteins?

They have no impact on protein function.

They are crucial for peptide bond formation.

They determine the primary structure of proteins.

They play a role in protein conformation and function. (correct)

Which of the following correctly describes the formation of a peptide bond?

It involves the hydrolysis of a protein.

It is formed through dehydration synthesis between the carboxyl group of one amino acid and the amine group of another. (correct)

It involves a reaction between two amine groups.

It occurs through a covalent bond between two identical amino acids.

How are the 20 proteinogenic amino acids primarily distinguished?

Their ability to form hydrogen bonds.

The unique side chains that impart specific properties. (correct)

Their molecular weight.

Their peptide bond formation capabilities.

What thermodynamic property is associated with the formation of a peptide bond?

It exhibits partial double bond character. (D) Signup and view all the answers

Which bonds are primarily involved in determining the rotatable conformations about the F and Y bonds in peptides?

Single C-N and C-C bonds in the peptide backbone. (A) Signup and view all the answers

In the Ramachandran plot, which angles are graphed to analyze protein conformations?

Phi (F) and psi (Y) angles. (C) Signup and view all the answers

Which of the following statements about amino acids is false?

Amino acids can only exist in one stereoisomeric form. (C) Signup and view all the answers

Which of the following correctly reflects the relationship between proteins and genes?

Genes encode the amino acid sequences that compose proteins. (D) Signup and view all the answers

What force is responsible for holding the two strands of the DNA double helix together?

Hydrogen bonds (D) Signup and view all the answers

Which non-covalent interaction is characterized by temporary dipoles due to fluctuating electron clouds?

Van der Waals interaction (B) Signup and view all the answers

What defines the dielectric constant for water compared to lipids?

Water has a higher dielectric constant. (D) Signup and view all the answers

Which of the following processes is NOT enabled by non-covalent reversible forces?

Formation of covalent bonds (B) Signup and view all the answers

What does the First Law of Thermodynamics state?

Energy can never be generated nor destroyed. (D) Signup and view all the answers

Which statement best describes entropy?

It reflects the degree of disorder or randomness. (B) Signup and view all the answers

What follows from the Second Law of Thermodynamics regarding spontaneous processes?

Total entropy increases. (D) Signup and view all the answers

Which of the following is a consequence of the temporary dipoles created in Van der Waals interactions?

They induce temporary dipoles in neighboring molecules. (D) Signup and view all the answers

How can entropy locally decrease according to thermodynamic principles?

If a local decrease is compensated by an equal or greater increase elsewhere in the universe. (A) Signup and view all the answers

What is the primary effect of the hydrophobic effect on proteins?

It favors the aggregation of nonpolar groups, increasing overall entropy. (D) Signup and view all the answers

Which statement about proteins is incorrect?

Proteins have a rigid structure only. (A) Signup and view all the answers

What characterizes motor proteins?

They facilitate movement within cells and organisms. (B) Signup and view all the answers

What is true about amino acids?

Only L-amino acids are found in natural proteins. (C) Signup and view all the answers

What determines the variable structures of proteins?

The type of side chains present in the amino acids. (B) Signup and view all the answers

In which instance do amino acids become structural components of proteins?

As they are linked by peptide bonds in a specific sequence. (C) Signup and view all the answers

What's the significance of chirality in amino acids?

Chiral amino acids can exist in two isomer forms, but only one enantiomer is found in nature. (B) Signup and view all the answers

Which of the following amino acid pairs are often found in cis configurations?

Tyr-Pro (C), Ser-Pro (D) Signup and view all the answers

What is the role of prolyl isomerase?

It facilitates the transition between different amino acid configurations. (C) Signup and view all the answers

What are the names of the two degrees of rotational freedom allowed by the rigid peptide bond?

Phi and Psi (A), F and Y (C) Signup and view all the answers

What limits the range of values for angles phi (F) and psi (Y) in protein folding?

Steric clashes (A) Signup and view all the answers

What percentage of all possible protein conformations are typically excluded by steric constraints?

75% of conformations (D) Signup and view all the answers

How are amino acids modified after protein synthesis?

By methylation and phosphorylation (D) Signup and view all the answers

Which type of interactions are crucial for stabilizing proteins?

Non-covalent interactions (D) Signup and view all the answers

What characterizes the peptide bond structure?

It is kinetically stable. (B) Signup and view all the answers

What is the effect of phosphorylation on proteins?

It can both activate proteins or keep them inactive. (C) Signup and view all the answers

Which enzyme is responsible for adding a phosphate group to a protein?

Kinase (C) Signup and view all the answers

Which amino acid is known to form disulfide bridges that stabilize protein structures?

Cysteine (C) Signup and view all the answers

What effect does mercaptoethanol have on proteins?

It reduces disulfide bridges to thiols. (D) Signup and view all the answers

What characterizes the peptide bond?

It demonstrates partial double bond character and rigidity. (A) Signup and view all the answers

Which configuration of the peptide bond is generally favored?

Trans configuration due to lower steric hindrance. (B) Signup and view all the answers

What is typically the starting point of a polypeptide chain?

N-terminus (B) Signup and view all the answers

How do peptide bonds contribute to protein structure?

They form rigid, planar units that define the backbone. (C) Signup and view all the answers

Which of the following amino acids has a side chain that is primarily non-polar?

Leucine (D) Signup and view all the answers

What is the main reason disulfide bridges are important in protein structure?

They provide stabilization and define protein conformation. (B) Signup and view all the answers

Which of the following statements is true regarding the pKa values of the amino acids?

pKa values identify the ionization of the side chain and backbone. (A) Signup and view all the answers

What classification does histidine fall under based on its side chain properties?

Basic (C) Signup and view all the answers

What is the primary mechanism by which peptide bonds are formed?

Condensation reaction resulting in the loss of water (A) Signup and view all the answers

Which property is NOT characteristic of peptide bonds?

They can rotate freely around the bond. (C) Signup and view all the answers

Study Notes

Lecture Overview

Course: Biochemistry I (PHBC 522)
Lecturers: Hans-Georg Breitinger, Mohamed Z. Gad, Sahar Mohamed, and others
Focus on concepts related to amino acids and peptides.

Learning Outcomes

Understanding fundamental concepts in Chemistry, Biology, and Thermodynamics relevant to Biochemistry.
Identifying functional groups and non-covalent interactions pertinent to Biochemistry.
Naming and drawing structures of the 20 proteinogenic amino acids.
Describing posttranslational modifications of amino acid side chains and their biological significance.
Understanding peptide bond formation, thermodynamic properties, and amino acid arrangements in peptide chains.
Analyzing rotatable conformations (F and Y bonds) and their implications for protein structure using Ramachandran plots.

Non-Covalent Interactions

Electrostatic Interactions (Salt Bridges): Depend on charge (q) and distance (r), affected by dielectric constant (D).
Dipole-Dipole Interactions: Involve polar molecules and can influence structure.
Van der Waals Forces (London Forces): Result from temporary dipoles; critical in non-polar molecule interactions.

Biological Relevance of Non-Covalent Forces

Essential for various molecular interactions including DNA double helix stability, protein folding into secondary structures, and enzyme-substrate interactions.
Supports functions of macromolecular machinery like ribosomes, actin filaments, and microtubules.

Thermodynamics in Biochemistry

First Law: Energy is conserved; it cannot be created or destroyed, only transformed.
Second Law: Entropy increases in spontaneous processes; local decreases in entropy must be offset by greater increases in the universe.

Hydrophobic Effect

Nonpolar molecules aggregate to decrease water solvation shell; enhances protein structural integrity despite entropy loss in folding.

Proteins Summary

Comprise 50% of E. coli's dry mass; integral to biological functions including catalysis and structural roles.
Comprised of amino acids containing varying functional groups leading to diverse properties.

Amino Acids

Defined by -COOH (carboxyl) and -NH2 (amino) groups.
Nomenclature uses alpha (α) to designate the carbon next to the carboxyl.

Proteinogenic Amino Acids

19 of 20 are chiral; biologically relevant forms are L-amino acids.
Side chains determine unique properties and functionality, including formation of disulfide bridges by cysteine.

pKa Values

Amino acids exhibit unique pKa values influencing their ionization state:
- Arginine: pKa1 = 2.00, pKa2 = 9.00, pKa3 = 13.20
- Aspartic Acid: pKa1 = 2.01, pKa2 = 9.82, pKa3 = 3.83

Peptide Bond Characteristics

Formed through condensation reaction, creating stable polypeptide chains.
Structure has partial double bond character, conferring rigidity and planarity.
Configuration is predominantly trans due to reduced steric hindrance, with exceptions involving proline.

Ramachandran Plot

Graphical representation of allowed φ (phi) and ψ (psi) torsion angles in peptide bonds, illustrating sterically allowed and unfavorable conformations.

Summary of Key Concepts

Biochemistry integrates principles from various chemistry disciplines to analyze biological macromolecules.
Proteins, built from amino acids, undergo thermodynamic and dynamic processes, crucial for maintaining life functions.

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Description

Welcome to the first lecture of Biochemistry I PHBC 522. In this course, we will explore foundational concepts and key biochemical processes essential for understanding the biological sciences. Join us as we delve into the fascinating world of biochemistry with your instructors and fellow students.