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Questions and Answers
What role do enzymes play in cells?
What role do enzymes play in cells?
- They provide structural support to the cell.
- They transport molecules across the plasma membrane.
- They store genetic information.
- They catalyze chemical reactions within the cell. (correct)
Why is the understanding of proteins essential for comprehending other biological processes?
Why is the understanding of proteins essential for comprehending other biological processes?
- Proteins are solely responsible for energy production.
- Proteins are involved in DNA replication processes exclusively.
- Proteins serve as genetic materials in all organisms.
- Proteins execute the majority of cell functions. (correct)
What is the significance of the arrangement of amino acids in a protein?
What is the significance of the arrangement of amino acids in a protein?
- It affects the protein's solubility in water.
- It dictates the speed of protein synthesis.
- It determines the three-dimensional shape of the protein. (correct)
- It defines the protein's primary function.
What is true about the evolutionary history of proteins?
What is true about the evolutionary history of proteins?
Which of the following is NOT a function performed by proteins?
Which of the following is NOT a function performed by proteins?
What type of proteins serve as molecular machines in cells?
What type of proteins serve as molecular machines in cells?
What is a common characteristic of all proteins?
What is a common characteristic of all proteins?
How do proteins affect molecular transport across the plasma membrane?
How do proteins affect molecular transport across the plasma membrane?
What is the primary structure of proteins composed of?
What is the primary structure of proteins composed of?
How are proteins typically written in terms of directionality?
How are proteins typically written in terms of directionality?
What is a key characteristic of long chains of amino acids in proteins?
What is a key characteristic of long chains of amino acids in proteins?
What defines a peptide in contrast to a protein?
What defines a peptide in contrast to a protein?
Which of the following sequences corresponds to a specific tripeptide mentioned?
Which of the following sequences corresponds to a specific tripeptide mentioned?
What term describes the end of a protein where the amino group is located?
What term describes the end of a protein where the amino group is located?
What type of bond is formed between amino acids to create a protein?
What type of bond is formed between amino acids to create a protein?
Which of the following statements is true regarding the structure of proteins?
Which of the following statements is true regarding the structure of proteins?
What type of regions do larger proteins often contain that act as flexible hinges between domains?
What type of regions do larger proteins often contain that act as flexible hinges between domains?
What is estimated about eukaryotic proteins regarding intrinsically disordered regions (IDRs)?
What is estimated about eukaryotic proteins regarding intrinsically disordered regions (IDRs)?
How does thermal energy affect protein conformation?
How does thermal energy affect protein conformation?
What role do the rapid fluctuations of proteins play in their function?
What role do the rapid fluctuations of proteins play in their function?
How many different polypeptide chains can theoretically be made from 20 amino acids in a chain of four amino acids?
How many different polypeptide chains can theoretically be made from 20 amino acids in a chain of four amino acids?
What factor predominantly influences the number of possible polypeptide chains a cell can theoretically create?
What factor predominantly influences the number of possible polypeptide chains a cell can theoretically create?
What characterizes the conformations of proteins in terms of their structure?
What characterizes the conformations of proteins in terms of their structure?
Why is the understanding of intrinsically disordered regions important in the study of protein function?
Why is the understanding of intrinsically disordered regions important in the study of protein function?
What type of bond is formed between amino acids in proteins?
What type of bond is formed between amino acids in proteins?
What is the configuration of the α-carbon atom in amino acids?
What is the configuration of the α-carbon atom in amino acids?
At neutral pH (pH 7), the amino group and carboxyl group of an amino acid are usually:
At neutral pH (pH 7), the amino group and carboxyl group of an amino acid are usually:
Which configuration exclusively comprises amino acids found in proteins?
Which configuration exclusively comprises amino acids found in proteins?
Which side chain variable in amino acids is represented by R?
Which side chain variable in amino acids is represented by R?
What happens to the C–N bond in a peptide bond?
What happens to the C–N bond in a peptide bond?
What are the mirror-image forms of amino acids called?
What are the mirror-image forms of amino acids called?
Which of the following describes the nature of NH3's stabilization?
Which of the following describes the nature of NH3's stabilization?
What is referred to as protein modules?
What is referred to as protein modules?
Which of the following correctly describes the structure of the protein domains mentioned?
Which of the following correctly describes the structure of the protein domains mentioned?
What is a significant evolutionary advantage of β sheet–based domains?
What is a significant evolutionary advantage of β sheet–based domains?
Which protein is specifically mentioned as being formed from two brown-colored domains?
Which protein is specifically mentioned as being formed from two brown-colored domains?
What role do the loops in protein domains play?
What role do the loops in protein domains play?
How do the N- and C-terminal ends of two of the protein domains illustrated relate to each other?
How do the N- and C-terminal ends of two of the protein domains illustrated relate to each other?
Which type of protein domain is referenced in relation to calcium-binding?
Which type of protein domain is referenced in relation to calcium-binding?
What feature promotes the utility of certain protein domains in evolution?
What feature promotes the utility of certain protein domains in evolution?
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Study Notes
Proteins
- Proteins are essential for cell function and constitute most of a cell's dry mass.
- They are the building blocks of cells and perform a wide range of functions, such as catalyzing chemical reactions (enzymes), controlling the passage of molecules (membrane proteins), carrying messages (signaling proteins), and acting as molecular machines (kinesin, topoisomerase).
- Proteins are structurally complex and sophisticated molecules, a product of billions of years of evolution.
- The location of each amino acid in a protein's sequence determines its three-dimensional shape.
Amino Acid Structure
- Amino acids have a general formula with a carboxyl group, an amino group, and a side chain (R group).
- There are 20 different amino acids found in proteins.
- At pH 7, both the amino and carboxyl groups are ionized.
- The α-carbon atom is asymmetric, resulting in two mirror-image isomers (L and D).
- Proteins contain exclusively L-amino acids.
Peptide Bonds
- Amino acids are joined together by peptide bonds, which are amide linkages.
- The four atoms involved in each peptide bond form a rigid planar unit.
- There is no rotation around the C–N bond in a peptide bond.
- The two single bonds flanking the peptide bond allow for rapid rotation, making long chains of amino acids flexible.
Protein Structures
- Proteins can have single or multiple domains, which are stable, independently folding units connected by short, relatively unstructured regions.
- These unstructured regions can act as flexible hinges and are known as intrinsically disordered regions (IDRs), which can be very long and have important functions in cells.
- All protein structures are dynamic and constantly interconvert between closely related conformations due to thermal energy.
- Protein function is highly dependent on these rapid fluctuations and its dynamic character.
Evolution of Protein Structures
- The vast number of possible polypeptide chains is enormous, but only a tiny fraction of these are actually found in nature.
- Evolution has selected for specific protein structures and functions, driven by selective advantages over evolutionary time periods.
- Some protein domains, like the SH2 domain, have been especially mobile during evolution, suggesting that they have versatile structures and can adapt to different functions.
- β sheet-based domains are particularly successful because they provide a framework for generating new binding sites by making small changes to their protruding loops.
- These domains can also be easily integrated into other proteins due to their N- and C-terminal orientations.
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