Biology Chapter 4: Protein Structure

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Questions and Answers

What is the primary structure of proteins?

The order in which amino acids are covalently linked (correct)

The ordered 3-D arrangement of backbone atoms

The 3-D arrangement of all atoms in a protein

The arrangement of subunits within a protein

Which level of protein structure involves the 3-D arrangement of all atoms, including those in prosthetic groups?

Secondary structure

Quaternary structure

Primary structure

Tertiary structure (correct)

What effect can a single change in the amino acid sequence have on a protein?

It will not affect the protein at all

It can enhance the protein's stability

It can change the protein's synthesis rate

It can alter the protein's biological functions (correct)

What are the native conformations of proteins?

The 3-D shapes of proteins with biological activity (C) Signup and view all the answers

Which statement best describes tertiary protein structure?

It is the complete 3-D structure of a single polypeptide chain (D) Signup and view all the answers

What is characterized by the arrangement of subunits in a protein?

Quaternary structure (C) Signup and view all the answers

Why can proteins have many different conformations?

Because of the flexibility of amino acids (A) Signup and view all the answers

Which type of structure is primarily concerned with the ordered 3-D arrangement of the protein backbone atoms?

Secondary structure (A) Signup and view all the answers

What stabilizes the α-helical regions in myoglobin (Mb)?

Hydrogen bonding in the polypeptide backbone (D) Signup and view all the answers

Which type of secondary structure is absent in myoglobin?

β-pleated sheets (D) Signup and view all the answers

Where are most polar side chains located in the structure of myoglobin?

Exterior of the protein (A) Signup and view all the answers

Which component is involved in interactions with the heme group in myoglobin?

Histidine residues (A) Signup and view all the answers

What occupies the fifth coordination site of the Fe(II) in the heme group?

Imidazole side chain of histidine residue F8 (C) Signup and view all the answers

What is the composition of the porphyrin ring in the heme group?

Four five-membered rings linked by methine groups (C) Signup and view all the answers

How many coordination sites does the heme group possess for the Fe(II)?

Six (A) Signup and view all the answers

What binds at the sixth coordination site of the heme group?

Oxygen (O2) (C) Signup and view all the answers

What is a βαβ unit comprised of?

Two parallel strands of β-sheet connected by α-helix (A) Signup and view all the answers

Which supersecondary structure is also known as a helix-turn-helix?

αα unit (C) Signup and view all the answers

What characterizes the β-meander supersecondary structure?

Formed by tight reverse turns connecting an antiparallel sheet (A) Signup and view all the answers

Which of the following is true about motifs in protein structure?

They represent repetitive supersecondary structures (B) Signup and view all the answers

How can a domain be defined?

A part of a polypeptide chain that can fold independently into a stable tertiary structure (C) Signup and view all the answers

What does it mean when it is said that domains are units of function?

Proteins can contain various types of domains associated with distinct functions. (C) Signup and view all the answers

What is the distinguishing feature of a β-barrel structure?

Results from extensive β-sheets folding back on themselves (B) Signup and view all the answers

Which statement correctly describes the Greek key motif?

It is formed when a polypeptide chain doubles back on itself. (B) Signup and view all the answers

What is the role of histidine F8 in relation to the iron in heme?

It occupies the fifth coordination site of the iron. (A) Signup and view all the answers

Which type of protein structure does hemoglobin represent?

Tetrameric (A) Signup and view all the answers

How does carbon monoxide (CO) compare to oxygen (O2) in terms of affinity for free heme?

CO has a higher affinity, 25,000 times greater than O2. (B) Signup and view all the answers

What structural characteristic defines oligomers?

Made up of several smaller subunits. (C) Signup and view all the answers

What property describes allosteric behavior in multisubunit proteins?

Conformational changes in one subunit affect others. (D) Signup and view all the answers

Which statement accurately describes hemoglobin's structure?

It has two α-chains and two β-chains. (D) Signup and view all the answers

What happens to carbon monoxide's advantage over oxygen when it binds at an angle?

It decreases by two orders of magnitude. (D) Signup and view all the answers

Which of the following is NOT a method of interaction between polypeptide chains in quaternary structures?

Covalent bond formation (A) Signup and view all the answers

What defines the tertiary structure of proteins?

The 3-D arrangement of all atoms in a molecule (B) Signup and view all the answers

Which interaction is NOT involved in stabilizing the tertiary structure of proteins?

Ionic bonding between identical charged side chains (C) Signup and view all the answers

What role do prosthetic groups play in the structure of myoglobin?

They provide a specific pocket for binding, affecting protein function. (A) Signup and view all the answers

In which type of protein is the backbone less likely to fold back on itself?

Fibrous proteins (A) Signup and view all the answers

What can restrict the folding patterns of polypeptide chains in proteins?

Disulfide bonds formed between cysteines (A) Signup and view all the answers

How do the side chains of amino acids influence the tertiary structure of proteins?

They help determine how helical and pleated-sheet sections fold back on each other. (B) Signup and view all the answers

What type of structure do helical and pleated-sheet sections create in proteins?

Secondary structure (C) Signup and view all the answers

Which of the following proteins contains disulfide bonds?

Chymotrypsin (D) Signup and view all the answers

Study Notes

Overview of Protein Structure

Proteins are polymers formed by amino acids linked by covalent peptide bonds.
Native conformations are the specific 3-D shapes that enable biological activity.
Proteins can have segments of random structure without obvious repeating patterns.

Levels of Protein Structure

Primary Structure (1°): The linear sequence of amino acids, read from N-terminal to C-terminal.
Secondary Structure (2°): The ordered 3-D arrangement of the polypeptide backbone, typically involving α-helices and β-sheets.
Tertiary Structure (3°): The overall 3-D arrangement of all atoms, accounting for side chains and any prosthetic groups.
Quaternary Structure (4°): The arrangement of multiple polypeptide subunits in relation to each other, forming larger functional complexes.

Primary Structure Insights

Amino acid sequences dictate protein conformation and function; single amino acid changes can significantly impact biological activity (e.g., sickle-cell anemia due to Glu6 → Val substitution in hemoglobin).
Supersecondary structures result from combinations of α- and β-strands.
- βαβ Unit: Two parallel β-strands connected by an α-helix.
- αα Unit: Two antiparallel α-helices, also known as a helix-turn-helix motif.
- β-Meander: Antiparallel β-sheets linked by tight reverse turns.
- Greek Key: A structural motif formed by a polypeptide chain looping back on itself.
Motifs offer insights into protein folding but do not predict function.
Domains are independently folding segments of polypeptides and units of function.

Tertiary Structure Details

Tertiary structure incorporates all atoms, including side chains and prosthetic groups.
Fibrous proteins have elongated, rod-like shapes, while globular proteins have more compact structures.
Forces Stabilizing Tertiary Structure:
- Noncovalent interactions (hydrogen bonds, hydrophobic interactions, electrostatic attractions).
- Disulfide bonds restrict folding patterns, varying between proteins (present in chymotrypsin but absent in myoglobin).

Myoglobin Structure

Myoglobin is composed of a single polypeptide with 153 amino acids and a heme prosthetic group within a hydrophobic pocket.
Exhibits eight α-helical regions and no β-pleated sheets.
Polar side chains reside on the exterior, while the interior contains mostly nonpolar side chains and polar histidines that interact with the heme group.
The heme group binds oxygen, with its conformation significantly influenced by the protein environment.

Heme Group Characteristics

Contains Fe(II) linked to an organic protoporphyrin IX structure, facilitating oxygen binding at the sixth coordination site.
Four coordination sites occupied by nitrogen atoms, with the fifth occupied by the imidazole side chain of histidine residue F8.
Oxygen has a weaker affinity than carbon monoxide; CO is a potent poison due to its high binding affinity.

Quaternary Structure Features

Comprises proteins with multiple polypeptide chains, referred to as subunits.
Oligomers include proteins like dimers, trimers, and tetramers, which interact primarily through noncovalent forces.
Allosteric properties allow conformational changes in one subunit to influence neighboring subunits, critical for functional regulation.

Hemoglobin Structure

Hemoglobin is a tetramer (α2β2), containing two α-chains and two β-chains.
Each chain has distinct lengths (141 residues for α and 146 for β).
Amino acid sequences of hemoglobin chains are homologous to myoglobin, illustrating evolutionary relationships among hemoproteins.

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Description

This quiz covers Chapter 4, focusing on the three-dimensional structure of proteins. It explores the different levels of protein structure, including primary, secondary, tertiary, and quaternary structures. Test your understanding of how these structures relate to protein function and biological activity.