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Questions and Answers
What are the most structurally complex and sophisticated molecules?
Proteins
What type of bond links amino acids together?
Covalent peptide bond
Which of the following determines the folding of protein chains?
What does the 3-D structure of a protein depend on?
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The final folded shape of a protein is that which maximizes its free energy.
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What assists proteins to fold in their correct shapes?
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Which structural feature is a result of hydrogen bonding between N-H and C=O?
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Alpha helices are abundant in cell membranes.
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What is an example of a protein that consists of amino acid sequence?
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What characterizes the primary structure of proteins?
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What is domain shuffling?
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Match the following protein structures to their descriptions:
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What are paralogs?
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Orthologs are proteins that have different functions in different organisms.
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What type of proteins are serine proteases?
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What is the role of the SH2 domain?
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What type of binding occurs at the binding site of a protein?
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Study Notes
Protein Structure
- Proteins are the most complex molecules.
- Amino acids are linked together by covalent peptide bonds.
- The polypeptide backbone consists of repeating sequences of atoms.
- Amino acid side chains are attached to the backbone and are not involved in peptide bonds.
- The folding of a protein chain is determined by noncovalent bonds.
- The 3-D structure of a protein is determined by its amino acid sequence.
- The final folded shape of a protein minimizes its free energy.
- The conformation of a protein can fluctuate due to thermal energy and interactions with other molecules.
- Molecular chaperones assist proteins in folding into their correct shapes.
Secondary Structure
- α-helix and β-sheet structures form due to hydrogen bonding between the N-H and C=O groups of the polypeptide backbone.
- α-helixes are abundant in cell membranes, with their nonpolar regions exposed and polar regions inside.
- β-sheets are parallel or antiparallel chains held by hydrogen bonds.
- α-helixes form when a single polypeptide chain twists into a cylinder with H-bonds between every fourth peptide bond.
- α-helixes can wrap around each other to form coiled coils, where the nonpolar parts of the two helices are on the inside.
Protein Domains
- Larger proteins consist of smaller protein domains.
- SH2 domains are involved in cell signaling and cause protein binding.
- Src protein kinase contains SH2, SH3, and a C-terminal domain for catalytic activity.
- Intrinsically disordered regions (IDRs) act as flexible hinges between domains.
- Proteins are constantly in motion, and this flexibility can expose binding sites for other molecules.
- Thousands of possible protein polypeptides exist, but only a small fraction are stable and found in cells.
Protein Families and Evolution
- Gene duplication allows gene copies to evolve independently, leading to new functions.
- Protein families are groups of proteins with similar structures and functions.
- Paralogs are proteins within the same species that evolved from gene duplication.
- Orthologs are proteins with the same function but found in different species.
- Serine proteases are a family of enzymes with similar structures but different functions.
Domain Shuffling
- Domain shuffling involves the accidental joining of DNA sequences, creating multidomain proteins.
- New binding surfaces arise where two domains meet.
- Protein modules are mobile domains that can move between different proteins, leading to diverse functions.
- Some domains with N and C terminals on opposite poles lead to extended structures.
- Other domains with N and C terminals close together are plug-in type, inserting into loops of other proteins.
Protein Binding
- Binding site: a region on a protein's surface that binds to another molecule through noncovalent bonds.
- Subunits: individual polypeptide chains that make up a protein complex.
- Dimer: a protein composed of two subunits.
- Haemoglobin, for example, contains two alpha globin subunits and two beta globin subunits.
Protein Classification
- Globular proteins: polypeptide chains that fold into a compact, spherical shape.
- Fibrous proteins: extended polypeptide chains, forming structures with high tensile strength.
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Description
This quiz explores the intricate details of protein structure, focusing on the formation of peptide bonds, the importance of amino acid sequences, and the roles of noncovalent bonds in determining protein folding. Additionally, the secondary structures such as α-helices and β-sheets are examined, showcasing their formation and characteristics. Test your knowledge on these essential concepts of biochemistry.
