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Questions and Answers
Ionic interactions involve negatively charged groups interacting with positively charged ______.
Ionic interactions involve negatively charged groups interacting with positively charged ______.
groups
Hydrophobic side chains aggregate on the inside of the protein while hydrophilic side chains are on the ______.
Hydrophobic side chains aggregate on the inside of the protein while hydrophilic side chains are on the ______.
outside
Proteins composed of a single polypeptide do not have ______ structure.
Proteins composed of a single polypeptide do not have ______ structure.
quaternary
The proteins known as ______ assist in the proper folding of other proteins during synthesis.
The proteins known as ______ assist in the proper folding of other proteins during synthesis.
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Chaperones keep proteins ______ until the synthesis process is finished.
Chaperones keep proteins ______ until the synthesis process is finished.
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Denaturation involves the unfolding of protein secondary and tertiary structure without hydrolysis of ______ bonds.
Denaturation involves the unfolding of protein secondary and tertiary structure without hydrolysis of ______ bonds.
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Proteins with two or more polypeptides are said to have a ______ structure.
Proteins with two or more polypeptides are said to have a ______ structure.
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Denatured proteins are usually ______ and precipitate from solution.
Denatured proteins are usually ______ and precipitate from solution.
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The first step in the folding process involves the formation of ______ structures.
The first step in the folding process involves the formation of ______ structures.
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Amyloidosis is a group of diseases occurring due to the aggregation of ______.
Amyloidosis is a group of diseases occurring due to the aggregation of ______.
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Positive and negative side chains attract each other, while similar charges are kept out of ______.
Positive and negative side chains attract each other, while similar charges are kept out of ______.
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Improperly folded proteins are usually ______ in the cell.
Improperly folded proteins are usually ______ in the cell.
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A monomeric protein consists of a single polypeptide folded into secondary and ______ structures.
A monomeric protein consists of a single polypeptide folded into secondary and ______ structures.
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Different secondary structures are connected by ______.
Different secondary structures are connected by ______.
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Globular proteins are compact with a high density ______.
Globular proteins are compact with a high density ______.
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A domain consists of different ______ structural elements.
A domain consists of different ______ structural elements.
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Folding of one domain is independent of other domains on the same ______.
Folding of one domain is independent of other domains on the same ______.
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Interactions stabilizing tertiary structure include covalent, ionic, and ______ interactions.
Interactions stabilizing tertiary structure include covalent, ionic, and ______ interactions.
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Disulfide bonds are produced from oxidation of the –SH group of two ______ residues.
Disulfide bonds are produced from oxidation of the –SH group of two ______ residues.
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Non-polar amino acids are located on the ______ of the protein.
Non-polar amino acids are located on the ______ of the protein.
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Hydrogen bonds are formed between amino acid side chains with oxygen- or nitrogen-bound ______.
Hydrogen bonds are formed between amino acid side chains with oxygen- or nitrogen-bound ______.
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Proteins are composed of ______ attached by peptide bonds.
Proteins are composed of ______ attached by peptide bonds.
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The four hierarchies of protein structure are primary, secondary, ______, and quaternary.
The four hierarchies of protein structure are primary, secondary, ______, and quaternary.
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A peptide bond is an amide link between the α-carboxyl group of one amino acid and the α-______ group of another.
A peptide bond is an amide link between the α-carboxyl group of one amino acid and the α-______ group of another.
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The N-terminal is written to the left and the C-______ is written to the right.
The N-terminal is written to the left and the C-______ is written to the right.
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Each amino acid component of a peptide chain is called a ______.
Each amino acid component of a peptide chain is called a ______.
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Hydrogen bonds are parallel to the ______ in an α-helix.
Hydrogen bonds are parallel to the ______ in an α-helix.
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A β-sheet can be formed from two or more different ______, or from the same polypeptide.
A β-sheet can be formed from two or more different ______, or from the same polypeptide.
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β-bends also called ______ turns, reverse the direction of a polypeptide chain.
β-bends also called ______ turns, reverse the direction of a polypeptide chain.
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The α-helix contains about ______ amino acids per turn.
The α-helix contains about ______ amino acids per turn.
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Proline is known to disrupt the ______ structure due to its unique structure.
Proline is known to disrupt the ______ structure due to its unique structure.
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Antiparallel sheets have polypeptide chains arranged with N- and C-______ alternating.
Antiparallel sheets have polypeptide chains arranged with N- and C-______ alternating.
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Nonrepetitive secondary structures have less repetitive structure than ______ and sheets.
Nonrepetitive secondary structures have less repetitive structure than ______ and sheets.
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Ionic interactions may affect the stability of α-helices and ______ in proteins.
Ionic interactions may affect the stability of α-helices and ______ in proteins.
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The only charged groups on a polypeptide are found at the N-terminal α-______ group and the C-terminal α-carboxyl group.
The only charged groups on a polypeptide are found at the N-terminal α-______ group and the C-terminal α-carboxyl group.
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Study Notes
Protein Structure
- Proteins are composed of amino acids linked by peptide bonds.
- Proteins have four levels of structure: primary, secondary, tertiary, and quaternary.
Primary Structure
- The sequence of amino acids in a protein is called the primary structure.
- Amino acids are joined by peptide bonds, which are amide linkages.
- Peptide bonds are strong and not easily broken by heat or urea concentrations.
- Peptide bonds are hydrolyzed by prolonged exposure to strong acids, bases, or high temperatures.
Naming Peptides
- A peptide is two or more amino acids linked by a peptide bond.
- The free amino end is the N-terminal, and the free carboxyl end is the C-terminal.
- Amino acid sequences are read from the N-terminal to the C-terminal.
- Each amino acid in a polypeptide chain is called a residue.
Characteristics of Peptide Bonds
- Peptide bonds have a partial double bond character, making them shorter and rigid than single bonds.
- They are planar, with no free rotation around the carbonyl carbon and amide nitrogen.
- They are typically in the trans-configuration due to steric interference between the R-groups of amino acids.
Polarity of Peptide Bonds
- The -C=O and -NH groups of the amide linkage are uncharged and do not accept or release protons.
- These groups are polar and can participate in hydrogen bonds.
- The only charged groups on a polypeptide are the N-terminal α-amino group, the C-terminal α-carboxyl group, and ionized groups in the side chains of amino acids.
Secondary Structure
- The polypeptide chain forms regular arrangements of amino acids located near each other.
- Three major secondary structures include the α-helix, β-sheet, and β-bend.
The α-Helix
- The α-helix is a spiral structure with a coiled polypeptide backbone.
- Amino acid side chains extend outward from the central axis to avoid steric interference.
- The α-helix is stabilized by hydrogen bonding between peptide-bond carbonyl oxygens and amide hydrogens.
- These hydrogen bonds are parallel to the helix, extending from the carbonyl oxygen of one peptide bond to the -NH group of the peptide bond four residues ahead.
- Each turn of the α-helix contains 3.6 amino acids.
- Certain amino acids can disrupt the α-helix, including proline (due to its secondary amino group), charged amino acids, and bulky or branched side chains.
The β-Sheet
- In the β-sheet, all peptide bond components are involved in hydrogen bonding.
- The surface of the β-sheet is pleated.
- Two or more polypeptide chains are arranged in an almost fully extended form.
- Hydrogen bonds form between the carbonyl oxygen and amide hydrogen of two adjacent polypeptides.
- β-sheets can be parallel or antiparallel, depending on the arrangement of the N- and C-termini of the polypeptide chains.
β-Bends (Reverse Turns)
- β-bends reverse the direction of the polypeptide chain.
- They are commonly found on the surface of proteins and often connect successive strands of parallel β-sheets.
- β-bends usually consist of four amino acids, with proline and glycine frequently found.
Nonrepetitive Secondary Structures
- Approximately half of proteins are organized into repetitive structures like α-helices and β-sheets.
- The remaining polypeptide chain has a loop or coil conformation called a "nonrepetitive secondary structure."
- Coils and loops are not random but have less repetitive structure than helices and sheets.
Supersecondary Structures (Motifs)
- Supersecondary structures are formed from the combination of different secondary structures (α-helices, β-sheets, and nonrepetitive sequences).
- These structures are connected by β-bends and are stabilized by interactions between side chains from adjacent secondary structures.
- Supersecondary structures that occur consistently in different proteins are called motifs.
Tertiary Structure
- Tertiary structure refers to the folding of domains and the final arrangement of domains.
- Globular proteins are compact with a high-density core.
- Hydrophobic side chains are buried in the interior of the protein, while hydrophilic groups are on the surface.
Tertiary Structure Domains
- Domains are functional units of polypeptides.
- Polypeptide chains longer than 200 amino acids consist of two or more domains.
- Each domain is structurally independent from other domains on the polypeptide chain.
Interactions Stabilizing Tertiary Structure
- Four types of interactions stabilize tertiary structure: disulfide bonds, hydrophobic interactions, hydrogen bonds, and ionic interactions.
- Disulfide bonds: Covalent bonds formed by the oxidation of -SH groups from two cysteine residues, creating cystine.
- Hydrophobic interactions: Interactions between amino acids with non-polar side chains, driving them to the interior of the protein.
- Hydrogen bonds: Formed between amino acid side chains with oxygen- or nitrogen-bound hydrogen and electron-rich atoms.
- Ionic interactions: Interactions between negatively charged groups (Asp or Glu) and positively charged groups (Lys).
Protein Folding
- Interactions between side chains of amino acids determine how a polypeptide chain folds into a three-dimensional shape.
- Proteins fold to attain a low-energy state, facilitated by attractions between opposite charges, aggregation of hydrophobic side chains, and hydrogen bonds.
- Protein folding often begins as the polypeptide chain is being synthesized to prevent misfolding.
Role of Chaperones in Protein Folding
- Chaperones (heat-shock proteins) are involved in the correct folding of proteins.
- They interact with the polypeptide at different stages of the folding process.
- Functions of chaperones include:
- Keeping the protein unfolded until synthesis is finished.
- Acting as catalysts to increase the rate of protein folding.
- Protecting unfolded portions of the protein as they fold, preventing misfolding.
Quaternary Structure
- Monomeric proteins consist of a single polypeptide folded into secondary and tertiary structure.
- Quaternary structure describes proteins with two or more polypeptides, called subunits.
- Subunits are held together by non-covalent interactions like hydrogen bonds, ionic bonds, and hydrophobic interactions.
- Subunits can function cooperatively or independently.
Isoforms
- Isoforms are proteins that have the same function but are encoded by different genes and have different primary structures.
Protein Denaturation
- Denaturation is the unfolding of protein secondary and tertiary structure without hydrolysis of peptide bonds.
- Denaturing agents include heat, organic solvents, detergents, acids, bases, and heavy metals.
- Denatured proteins are usually permanently disordered and insoluble.
Protein Misfolding
- Improperly folded proteins are usually degraded in the cell.
- Accumulation of misfolded proteins can lead to disease.
- Amyloidoses are a group of diseases caused by the aggregation of amyloids, which are fibrillar proteins composed of β-sheets.
- Amyloid accumulation is implicated in diseases like Alzheimer's disease.
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Description
This quiz covers the fundamental concepts of protein structure, emphasizing the importance of peptide bonds and amino acid sequences. Understand the four levels of protein structure and the characteristics of peptide bonds that influence protein stability and function.
