protein structure Flashcards
Define hydrogen bonds in the context of biochemistry.
Hydrogen bonds are interactions between permanent dipoles where one dipole includes a hydrogen atom and the other has a lone pair of electrons or a negative charge, with the hydrogen atom partly shared between a donor and an acceptor atom.
How do van der Waals forces contribute to protein structure?
Van der Waals forces arise from interactions between dipoles and charges, operating as a net attractive force between molecules, particularly when their shapes fit well together.
Explain the significance of hydrophobicity in protein stability.
Hydrophobicity is significant because non-polar molecules cannot join the hydrogen bond network and are excluded, while polar molecules can bond and are soluble, which is crucial for the stability of proteins.
What role do polar and non-polar molecules play in the hydrogen bond network?
Polar molecules can join the hydrogen bond network and are hydrophilic, while non-polar molecules are hydrophobic and cannot join the network, leading to their exclusion.
Describe the importance of weak forces in biochemistry.
Weak forces, such as hydrogen bonds and van der Waals forces, are crucial for the interactions and stability of protein structures.
What is the relationship between hydrophilic and hydrophobic parts in some molecules?
Some molecules, like lipids, have both hydrophilic and hydrophobic parts, which influences their behavior in biological systems.
Define amphipathic molecules.
Molecules that have both hydrophilic (water-attracting) and hydrophobic (water-repelling) properties.
Describe the characteristics of polar and non-polar groups in proteins.
Polar groups, such as those containing OH, NH, or CO, are hydrophilic and can form hydrogen bonds, while non-polar groups, consisting only of CH, are hydrophobic.
How many basic building blocks are there in proteins?
There is one basic building block, the α amino acid, with twenty variations.
Describe the secondary structure of proteins.
The secondary structure consists of regular arrangements of the polypeptide chain, such as α helices and β strands.
What is the primary structure of a protein?
The primary structure is the amino acid sequence of the protein, which is one-dimensional and represents a list of the amino acids.
What forms the tertiary structure of a protein?
The tertiary structure is formed by the folding together of collections of linked secondary structure elements into a complete folded sequence.
Define quaternary structure in proteins.
The quaternary structure is formed when subunits aggregate together to create a biologically active molecule.
What is the role of the α carbon in amino acids?
The α carbon is tetrahedral and forms single covalent bonds with four surrounding atoms, including a variable side chain (R).
How many amino acids can be present in a protein?
A protein may contain as few as 50 or as many as 1000 or more amino acid building blocks.
What is the relationship between the primary structure and the protein’s function?
The primary structure, or amino acid sequence, directly influences the protein’s character and function.
Describe the process of protein folding from primary to tertiary structure.
The primary structure folds into secondary structures, which then combine into motifs, ultimately forming the tertiary structure.
Describe the primary structure of proteins.
The primary structure of proteins refers to the amino acid sequence, which is a list of the amino acids joined together in long chains.
How does the amino acid sequence affect protein properties?
The amino acid sequence determines all structural and functional properties of the protein.
Identify the average length of protein sequences in prokaryotes and eukaryotes.
Prokaryotic protein sequences average around 212 residues, while eukaryotic protein sequences average about 280 residues.
Explain the significance of protein sequence knowledge in structure determination.
Knowledge of the protein sequence is vital for understanding its function and can aid in structure determination, although it may not provide direct information about the three-dimensional structure.
Define the relationship between mutations and genetic diseases.
Mutations, which are changes in the amino acid sequence, can lead to genetic diseases by altering the function of proteins.
How does sickle cell anemia illustrate the impact of a single amino acid mutation?
Sickle cell anemia is caused by a mutation in hemoglobin where one amino acid changes (glu6 to val6), resulting in less soluble hemoglobin and distorted red blood cells.
What is the effect of a 3 base deletion in the gene for cystic fibrosis?
A 3 base deletion in the cystic fibrosis gene removes one amino acid (phenylalanine) from the protein product, affecting its function.
Describe the distribution of amino acids in protein sequences.
Amino acids occur with varying frequencies, with some amino acids appearing more frequently than others, indicating a non-random distribution in longer stretches of sequence.
What is the typical range for protein sequence lengths?
Most protein sequences range from 200 to 500 residues in length, although some can be as long as 25,000 residues.
How are proteins related to other proteins in terms of structure?
Understanding how a protein is related to other proteins can provide insights into its function and structural characteristics, especially if it belongs to a well-characterized family.
Describe how genetic defects can affect future generations.
Genetic defects causing serious disease but which are not lethal can be passed on to future generations.
Define the primary structure of proteins.
The primary structure of proteins refers to the sequence of amino acids linked together in a polypeptide chain.
How are amino acids structured?
Amino acids consist of an amino group, an acidic group, and a central carbon (α carbon) linked by single bonds to four surrounding atoms, with a variable side chain (R) that differentiates the 20 amino acids.
Explain the process of forming a peptide bond.
A peptide bond is formed through a condensation reaction between the amino and acidic groups of amino acids, resulting in the elimination of water.
What is meant by the term ‘residues’ in protein structure?
Amino acids linked together in a protein chain are often referred to as ‘residues’.
Describe the characteristics of the peptide bond.
The peptide bond has double bond character, allowing no rotation about the bond, and the atoms involved are all in a plane, known as the peptide plane.
