CHAPTER 2 and 4 - Q & A
Fatty acids are said to be "amphipathic." What is meant by this term and how does an amphipathic molecule behave in water?
Amphipathic molecules have both a hydrophilic and a hydrophobic end. Their hydrophilic end can hydrogen- bond to water, but their hydrophobic end is repelled form water because it interferes with the water structure. So the hydrophobic ends of amphipathic molecules tend to be exposed to air at air- water interfaces or in the interior of an aqueous solution, they will always cluster together to minimize their contact with water molecules.
Why is polymer brush attributed to neurofilament proteins assembled into long, intermediate filaments found in abundance running along the length of nerve cell axons. The C- terminal region of these proteins is an unstructured polypeptide, hundreds of amino acids long and heavily modified by the addition of phosphate groups.
Because of the lack of secondary structure, the C- terminal region of he neurofilament proteins undergoes continual Brownina motion. The high density of negatively charged phosphate groups means that the C- terminals also experience repulsive interactions, which cause them to stand out from the surface of the neurofilament like the bristles of a brush.
Explain how phosphorylation and binding of a nucleotide such as ATP OR GTP can both be used to regulate protein activity. What do you suppose are the advantages o either form of regulation?
Both nucleotide binding and phosphorylation can induce allosteric changes in proteins. These can have a multitude of consequences such as altered enzyme affinity, drastic shape changes, and changes in affinity for other proteins or small molecules. Both mechanism are quite versatile. An advantage of nucleotide binding is the fast rate with which a small nucleotide can diffuse to the protein; the shape changes that accompany the function of motor proteins for example, require quick nucleotide replenishment. If the different conformational states of a motor protein were controlled by phosphorylation for example, a protein kinases would either need to diffuse into position at each step, a much slower process, or be associated permanently with each motor protein. One advantage of phosphorylation is that it requires only a single amino acid on the protein's surface, rather than a specific binding site. Phosphates can therefore be added to many different side chains on the same protein thereby vastly increasing the complexity formulation that can be achieved for single protein.
What common feature of a helices and beta sheets make them universal building blocks for proteins?
In an a helix and in the central strands of a beta sheet, all of the N-H and C=O groups in the polypeptide backbone are engaged in hydrogen bonds. This gives considerable stability to these secondary structural elements and it allows them to form in many different proteins.
Why could covalent bonds not be used in place of non covalent bonds to mediate most of the interactions of macromolecules?
Many of the functions that macromolecules perform rely on their ability to associate with and dissociate form other molecules readily. This allows cells to remodel their interior when they move or divide and to transport components from one organelle to another. Covalent bonds would be too stable for such a purpose, requiring a specific enzyme to break each kind of bond.
Protein structure is determined solely by a protein's amino acid sequence. Should a genetically engineered protein in which the original order of all amino acids is reversed have the same structure as the original protein?
NO it would not have the same or even a similar structure because the peptide bond has a polarity. Looking at two sequential amino acids in a polypeptide chain, the amino acid that is closer to the N-terminal end contributes the carboxyl group and the other amino acid contributes the amino group to the peptide bond that links the two amino acids. Changing their order would put the side chains into different positions with respect to the peptide backbone and therefore change the way the polypeptide folds.
What are the forces that determine the folding of a macromolecule into a unique shape?
Non covalent bonds form between the covalently linked subunits of a macromolecule such as a polypeptide of RNA chain causing the chain to fold into a unique shape. These noncovalent bonds include hydrogen bonds, ionic interactions, van der Waals attractions, and hydrophobic interactions. Because these interactions are weak, they can be broken with relative ease so most macromolecules can be unfolded by heating due to increased thermal motion.
What is meant by polarity of a polypeptide chain and by polarity of a chemical bond?
Polarity in a peptide chain refers to directional asymmetry- for example, in linear polymers such as polypeptides or nucleic acids. Both the covalent bonds that link the subunits together form only between the amino and the carboxyl groups of the amino acids in a polypeptide and between the 3' and 5' ends of the nucleotides in a nucleic acid, polypeptides and nucleic acids always have two different ends, which give the chain a defined chemical polarity. Polarity also refers to a separation of electric charge in a bond or molecule. This kind of polarity promotes hydrogen-bonding to water molecules and because of the water solubility, or hydrophilicity of a molecule it depends upon its being polar.
What can control protein activity by causing a conformational change?
Protein phosphorylation- involves the enzyme- catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed in protein kinase.
Hair is composed largely of fibers of the protein keratin. Individual keratin fibers are covalently cross- linked to one another by many disulfide (S-S) bonds. If curly hair is treated with mild reducing agents that break a few of the cross-links, pulled straight and then oxidized again, it remains straight. What do you think would happen if hair were treated with strong reducing agents that break all the disulfide bonds?
Strong reducing agents that break all of the S-S bonds would cause all the keratin filaments to separate. Individual hairs would be weakened and fragment. Mild reducing agents are used in treatments that either straighten or curl hair
How is it possible for a change in a single amino acid in a protein of 1000 amino acids to destroy its function, even when the amino acid is far away from any ligand-binding site?
The atoms at the biding sites of proteins must be precisely located to fit the molecules that they bind. Their location in turn requires the precise positioning of many of the amino acids and their side chains in the core of the protein, distant form the binding site itself. So even a small charge in their core can disrupt protein function by altering the conformation at a bind site far away
What happens when to a mutant enzyme when the temperature increases?
The heat- inactivation of the enzyme suggest that the mutation causes the enzyme to have a less stable structure. For example, a hydrogen bond that is normally formed between two amino acid side chains might no longer be formed because the mutation replaces one of these amino acids with a different one that cannot participate in the bond.Lacking such a bond that normally helps to keep the polypeptide chain folded properly, the protein partially or completely unfolds at a temperature at which it would normally be stable. Polypeptide chains that denature when the temperature is raised often aggregate, and they rarely refold into active proteins when the temperature is decreased.
What is involved in a motor protein moving along protein filaments in the cell?
The motor protein can move easily to the left as to the right and will not move steadily in one direction. If just one of the steps is coupled to ATP hydrolysis - ex by making detachment of one foot dependent on binding of ATP and coupling the reattachment to hydrolysis of the bound ATP, then the protein will show unidirectional movement that requires the continual consumption of ATP. Usually it doesn't matter which step is coupled to ATP hydrolysis.
What if anything is wrong with the following statement: " When NACL is dissolved in water, the water molecules closest to the ions will tend to preferentially orient themselves so that their oxygen atoms face the sodium ions and face away form the chloride ions"?
The statement if correct: the hydrogen-oxygen bond in water molecules is polar so that the oxygen atom carries a more negative charge than the hydrogen atoms. These partial negative charges are attracted to the positively charged sodium ions but are repelled from the negatively charged chloride ions.
Discuss whether the following statement is correct: "An ionic bond can, in principle, be thought of as a very polar covalent bond. Polar covalent bonds, then fail somewhere between ionic bonds at one end of the spectrum and non-polar covalent bonds at the other end."
The statement is right: Both ionic and covalent bonds are based on the same principles: Electrons can be shared equally between two interacting atoms, forming a nonpolar covalent bond; electrons can be shared unequally between two interacting atoms, forming a polar covalent bond; or electrons can be completely lost form on atom and gained by the other, forming an ionic bond. There are bonds of every conceivable intermediate state and for borderline cases it becomes arbitrary whether a bond is described as a very polar covalent bond or an ionic bond.
Urea is a molecule that disrupts the hydrogen- bonded network of water molecules. Why might high concentrations of urea unfold proteins?
Urea is a very small organic molecules that functions both as an efficient hydrogen- bond donor through its -NH2 group and as an efficient hydrogen- bond acceptor through its -C=O group. As such, it can squeeze between hydrogen bonds that stabilize protein molecules and thus destabilize protein structures. The nonpolar side chains of a protein are held together in the interior of the folded structure because they would disrupt the structure of water if they were exposed. At high concentrations of urea, the hydrogen- bonded network of water molecules becomes disrupted so that these hydrophobic forces are significantly diminished. Proteins unfold in urea as a consequence of its effect on these two forces.
Which of the two bonds would form between two hydrogens bound to carbon atoms, between a nitrogen atom and a hydrogen bound to a carbon atom, and between a nitrogen atom and a hydrogen bound to an oxygen atom?
Van der Waals in all and hydrogen bonds form only between the nitrogen atom and a hydrogen bound to an oxygen atom.
Describe the similarities and differences between van der Waals attractions and hydrogen bonds.
hydrogen bonds form between two specific chemical groups; one is always a hydrogen atom linked in a polar covalent bond to an oxygen or a nitrogen atoms, and the other is usually a nitrogen or an oxygen atom. Van der Waals attractions are weaker and occur between any two atoms that are in close enough proximity. Both hydrogen bonds and Van der Waals attractions are short- range interactions that come into play only when two molecules are already in close proximity. Both types of bonds can therefore be thought of a means of "fine-tuning" an interaction- helping to position two molecules correctly with respect to each other once they have been brought together by diffusion.
