chapter 4

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Questions and Answers

What is the main factor that determines the tertiary structure of a protein?

  • The hydrophobic effect (correct)
  • The sequence of amino acids in the polypeptide chain
  • The interactions between side chains
  • The presence of disulfide bonds

Which type of secondary structure is characterized by a rod-like shape with a tightly coiled backbone?

  • Loop
  • Turn
  • Alpha helix (correct)
  • Beta pleated sheet

Which of the following amino acids destabilizes alpha helices because it lacks an NH group and its ring does not fit into the helix?

  • Threonine
  • Valine
  • Isoleucine
  • Proline (correct)

What is the primary difference between parallel and antiparallel beta sheets?

<p>The direction of the polypeptide strands (D)</p> Signup and view all the answers

What is the role of turns and loops in protein structure?

<p>To facilitate interactions with other proteins (A)</p> Signup and view all the answers

What is the main difference between tertiary and quaternary structure?

<p>Tertiary structure involves interactions between side chains, while quaternary structure involves interactions between subunits (D)</p> Signup and view all the answers

Which of the following statements about denatured proteins is TRUE?

<p>They cannot refold into their original shape (A)</p> Signup and view all the answers

Which of the following is NOT a type of weak interaction that stabilizes quaternary structure?

<p>Covalent bonding (D)</p> Signup and view all the answers

What is the significance of the statement "Sequence specific conformation"?

<p>The amino acid sequence determines the three-dimensional structure of a protein (A)</p> Signup and view all the answers

Which of the following is TRUE about the peptide bond?

<p>It has a partial double bond character, making it relatively rigid (C)</p> Signup and view all the answers

What type of bond forms between amino acids in a polypeptide chain?

<p>Peptide bonds (D)</p> Signup and view all the answers

Which part of the polypeptide chain is known as the N-terminal?

<p>The beginning amino group (A)</p> Signup and view all the answers

What is the main significance of the amino acid sequence in a protein?

<p>It dictates the three-dimensional structure of the protein. (C)</p> Signup and view all the answers

Which type of reaction is involved in the formation of peptide bonds?

<p>Dehydration synthesis reaction (B)</p> Signup and view all the answers

What type of protein structure is characterized by a linear sequence of amino acids?

<p>Primary structure (C)</p> Signup and view all the answers

Which of the following plays a critical role in stabilizing protein structures?

<p>Hydrogen bonds between the main chain and side chains (B)</p> Signup and view all the answers

What is a characteristic of disulfide bonds in proteins?

<p>They involve the loss of electrons during oxidation of cysteine residues. (C)</p> Signup and view all the answers

Oligopeptides are defined as peptides with how many amino acids?

<p>Less than 50 amino acids (C)</p> Signup and view all the answers

What kind of structural feature does the R group in amino acids represent?

<p>The variable side chain of the amino acid (C)</p> Signup and view all the answers

Why is knowing amino acid sequences crucial in understanding diseases?

<p>It provides insight into abnormal protein function and diseases linked to sequence changes. (A)</p> Signup and view all the answers

Flashcards

Primary Structure of a Protein

The linear sequence of amino acids in a polypeptide chain, determined by the genetic code.

Secondary Structure of a Protein

The three-dimensional arrangement of a polypeptide chain, formed by hydrogen bonding between backbone atoms. Common secondary structures include alpha-helices and beta-sheets.

Tertiary Structure of a Protein

The overall three-dimensional shape of a protein, determined by interactions between side chains of amino acids. It is often described as the arrangement of secondary structural elements within a single polypeptide chain.

Quaternary Structure of a Protein

The structure formed when two or more polypeptide chains (subunits) come together to form a functional protein. Each subunit can have its own tertiary structure.

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Peptide Bond

The chemical bond that links amino acids together in a polypeptide chain. It is formed between the carboxyl group of one amino acid and the amino group of the next amino acid.

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Alpha Helix

A regular, spiral-shaped structure in proteins formed by hydrogen bonding between backbone atoms. It is characterized by a tightly coiled backbone with side chains extending outward.

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Beta Sheet

A flat, sheet-like structure in proteins formed by hydrogen bonding between polypeptide strands. It can be parallel or antiparallel, depending on the direction of the strands.

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Protein Folding

The process by which a protein folds into its three-dimensional shape, driven primarily by the hydrophobic effect. This process can be aided by chaperone proteins.

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Denatured Protein

A protein that has lost its normal shape and function due to changes in temperature, pH, or other environmental factors.

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Sequence Specific Conformation

The principle that the sequence of amino acids in a protein determines its three-dimensional structure, which in turn determines its function.

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Primary Structure

The linear sequence of amino acids in a polypeptide chain. It is determined by the genetic code and dictates the overall structure and function of the protein.

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Polypeptide Chain

A chain of amino acids linked together by peptide bonds. It has directionality, with an amino-terminal (N-terminal) and a carboxyl-terminal (C-terminal).

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Main Chain/Backbone

The regularly repeating portion of the polypeptide chain. It consists of the amino group, α carbon with hydrogen, and carboxyl group. These groups are involved in hydrogen bonding, contributing to the overall stability of the protein.

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Side Chain

The variable portion of a polypeptide chain. It is represented by the R group of each amino acid and determines the unique properties and functions of the protein.

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Disulfide Bond

A type of covalent bond that forms between two cysteine residues. It is important for stabilizing protein structure by creating loops and cross-links within or between polypeptide chains.

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Proteins

Polypeptides typically contain 50-2000 or more amino acids.

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Oligopeptides/Peptides

Polypeptides containing less than 50 amino acids

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Importance of Amino Acid Sequences

The knowledge of amino acid sequences is crucial for understanding and analyzing protein structure and function. It is also essential for studying abnormal functions and diseases resulting from changes in the sequence.

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Relationship between Amino Acid Sequence & Protein Function

The amino acid sequence determines the three-dimensional structure of a protein, influencing its biological activity. Any change or mutation in the sequence can lead to altered protein function or even dysfunction.

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Study Notes

Protein Three-Dimensional Structure

  • Protein structure is described at four levels: primary, secondary, tertiary, and quaternary.
  • Understanding protein structure is crucial to understanding its function.

Primary Structure

  • Amino acids are linked by peptide bonds.
  • Peptide bonds form a linear chain.
  • Formation of a peptide bond is a dehydration synthesis reaction, losing a water molecule in the process.
  • Peptide bonds are very stable.
  • Polypeptide chains have directionality (polarity), with an amino-terminal (N-terminal) and a carboxyl-terminal (C-terminal) end.

Secondary Structure

  • Polypeptide chains fold into regular structures, including alpha helices and beta pleated sheets.
  • Alpha helices are a rod-like structure stabilized by intrachain hydrogen bonds.
  • Hydrogen bonds form between the NH and CO groups of amino acids within the chain.
  • Beta pleated sheets are formed from two or more extended polypeptide strands, linked together by hydrogen bonds.
  • Beta sheets can be antiparallel (strands run in opposite directions) or parallel (strands run in the same direction).
  • Loops and turns are found on the protein surface, interacting with other proteins or the environment.

Tertiary Structure

  • Tertiary structure is the spatial arrangement of amino acids that are far apart in the primary sequence.
  • Protein folding is driven by the hydrophobic effect (hydrophobic side chains are buried inside, while polar, charged side chains are on the surface).
  • Van der Waals interactions between hydrophobic side chains stabilize protein structures.
  • Disulfide bonds are also important interactions in the tertiary structure, forming between cysteine residues.

Quaternary Structure

  • Quaternary structure involves the arrangement of subunits (single polypeptide chains) within a single protein.
  • Subunits interact via weak interactions, including hydrogen bonds, ionic bonds, and van der Waals forces.
  • Proteins can be composed of identical subunits or different subunits and vary in the number of subunits.

The Amino Acid Sequence Determines Protein Structure

  • Proteins can lose their shape and function (denature) under certain conditions, but they can also refold under specific conditions.
  • Some proteins require chaperones for proper refolding.
  • The amino acid sequence dictates the final, three-dimensional conformation, which dictates how it functions.

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