The Structure of Proteins

  1. The α-carbon (Cα) of an amino acid has _____ substituents, distinct from each other except in the case of the simplest amino acid, ________. Name the four substituents.
    • four 
    • glycine
    • an amino group, a carboxyl group, a proton and an R-group (aka side chain)
  2. Because the four substituents are distinct, the ____ is the chiral center. Amino acids that occur in ordinary proteins all have the ____ configuration though ____ amino acids are present in other kinds of molecules.
    • α-carbon 
    • L
    • D
  3. The properties of the ____ _____determine the specific characteristics of an amino acid. The ______ of the group which correlates with its solubility in water, is one critical property, _____ is another.
    • R group 
    • polarity 
    • size
  4. It is useful to cluster the R groups of the _____ genetically encoded amino acids into the following categories: (3)
    20 

    • Neutral (uncharged) and nonpolar
    • Neutral and polar
    • Charged
  5. The size aka ________ of the _____ _____ is of particular consequence for nonpolar amino acids because these ______ _____ pack into the compact interior of a protein, and is the reason the functional roles in proteins of (say) glycine and alanine are quite different from those of phenylanine and tryptophan.
    • volume
    • side chains
    • side chains
  6. Tryptophan although largely nonpolar, has a _____ _____ group that gives it a degree of polar character, and tyrosine, although classified as ______ because of its OH group, is much ______ so than serine. So keep in mind, boundaries between groups are _____ sharp than nomenclature might imply
    • hydrogen bonding
    • polar 
    • less
    • less
  7. The charged R groups are either ________ or ________ charged at neutral pH. This property is particularly important for its role at the _____ _____ of many enzymes. **Name two examples of negatively charged vs positively charged at neutral pH
    • negatively charged: aspartic acid and glutamic acid
    • positively charged: lysine, arginine and histidine
    • catalytic sites
  8. Peptide bonds
    covalent links between amino acids in a protein
  9. A peptide bonds forms by a ________ reaction, with elimination of a ______ molecule. It is a special case of an amide bond, each amino acid can form _____ such bond, so that successive links of the same kind can create a linear _____ ______
    • condensation reaction
    • water 
    • two 
    • polypeptide chain
  10. Because formation of each peptide bond includes elimination of a _____, the components of the chain are known as _____ ______ _________, or just _______ when amino acid is evident from context.
    • water
    • amino acid residues 
    • residues
  11. ______, _____ and _____ have special properties. For instance, because the R group is just a proton, ______ is not chiral, and it has much more _________ freedom than any other amino acid.
    • Glycine, proline and cysteine
    • glycine 
    • conformational
  12. Proline, in which the side chain has a _______ bond with N as well as Cα (making it an _____ acid) has less ______ ______ than many other amino acids. Moreover, absence of the _______ bonding potential of an NH group restricts its participation in _______ strutures
    • covalent 
    • imino acid
    • conformational freedom
    • hydrogen 
    • secondary
  13. Cysteine, with a ______ group on the side chain, is the one amino acid that is sensitive to ________-_______ under roughly physiological conditions. Two cysteines, correctly positioned across from each other in a folded protein, can form a _______ bond.
    • sulfhydryl group 
    • oxidation-reduction
    • disulfide bond
  14. How is the disulfide bond formed?
    by oxidation of the two SH groups to S-S
  15. The resulting pair of amino acids, linked by the S-S covalent bridge, is sometimes called _______.
    cystine
  16. All molecular phenomena in living systems depend on their _______ environment. The importance of the distinction between polar and nonpolar amino acid side chains comes from their properties with respect to ______ as a ______.
    • aqueous
    • water as a solvent
  17. Compare the side chains of aspartic acid and phenylalanine, whihc resemble _____ acid and ______, respectively, linked to the peptide main chain. ______ acid is very soluble in water; _______ is very insoluble. An aspartic acid side chain is therefore called ________ and a phenylalanyl side chain _________.
    • acetic acid
    • toluene 
    • Acetic acid 
    • toluene
    • hydrophilic 
    • hydrophobic
    • **even hydrophilic side chains can have hydrophobic parts (lysine)
  18. Water is an extensively ______ bonded liquid. Each water molecule can donate ____ ______ bonds and accept _____ _____ bonds.
    • hydrogen
    • two hydrogen 
    • two hydrogen
  19. The way in which a solute affects the hydrogen bonding of the surrounding water determines its ________ or _______ character.
    hydrophilic or hydrophobic
  20. _______ molecules perturb the network of hydrogen bonds; ________ molecules participate in it. Thus, it is more favorable for _______ molecules to remain adjacent to each other (________) than to disperse into an aqueous medium (_______).
    • Hyrophobic 
    • hydrophilic 
    • hydrophobic 
    • insoluble
    • soluble
  21. The sequence of amino acids in a real protein has evolved so that hydrophic  and hydrophilic tendencies cause the polypeptide chain to ____ ___, concealing _______ residues and exposing _______ residues.
    • fold up
    • hydrophobic 
    • hydrophilic
  22. In analyzing and desecribing the structure of proteins, it is useful to distinguish four levels of organization. Name them
    • primary structure
    • secondary structure
    • tertiary structure
    • quaternary structure
  23. The first level, the primary structure of a protein, is simply the sequence of _____ _____ _____ in the polypeptide chain. The _____ ______ specifies the primary structure of a protein directly. The primary structure is thus just a ______ dimensional string, specifying a ______ of chemical bonds
    • amino acid residues
    • genetic code
    • one (1D)
    • pattern
  24. The remaining three levels  depend on a protein's ______ _______ characteristics.
    three dimensional
  25. The secondary structure of a protein refers to the _______ _________ of its polypeptide chain, the ______ ________ arrangement of a short stretch of amino acids residues.
    • local conformation
    • three dimensional
  26. There are _____ very regular secondary structures found frequently in naturally occuring proteins, because these two local conformations are particularly stable for a chain of ______ _____. One of these is called the _____ ______ and the other is called the _____ ______
    • two 
    • L-amino acids
    • α helix
    • β strand
  27. In the α conformation, the polypeptide backbone spirals in a right handed sense around a _______ axis, so that _______ bonds form between the main chain _______ group of one reside and the ____ ____ _____ group of a residue four positions further along the chain.
    • helical 
    • hydrogen 
    • carbonyl group
    • main chain amide group
  28. The β strand conformation is an extended conformation, in which the side chains project _________ to either side of the backbone, and the amide and carbonyl groups project _______, also _________. The backbone is not quite fully stretched, so that the strand has a slightly ______ or _______ character.
    • alternately
    • laterally
    • alternating
    • zigzag or pleated character
  29. In folded proteins, _____ ______ form sheets joined by ______ bonds in the _____ _____
    • β strands
    • hydrogen bonds
    • main chain
  30. In the sheets, either _______ or _________ ________ bonding patterns are possible. What are they called respectively?
    • parallel or antiparallel hydrogen bonding
    • parallel or antiparallel β-pleated sheets
  31. In real proteins, various mixed sheets are often found rather either strictly _________ strand directions or strictly _________ ones.
    • alternating
    • unidirectional
  32. The tertiary structure of a protein refers to the usually ______ 3D folded arrangement that the polypeptide chain adopts under _________ conditions. Segments of the chain may be ____ _____ or ____ ______; the rest have less ________ conformations
    • compact
    • physiological
    • α helices or β strands
    • regular
  33. State an example of the less regular conformations
    turns or loops between secondary structure elements that allow these elements to pack tightly against each other
  34. Tertiary structures are not easily ________, and are _______ to assess how the protein/virus interacts with other molecules. This structure has a huge ______ power.
    • predictable
    • crystallized 
    • computer
  35. Usually, the _________ of the secondary and tertiary structures of a polypeptide chain depend on each other.
    stabilities
  36. Many proteins are composed of more than one polypeptide chain: _______ _______ refers to the way individual, folded chains associate with each other
    quaternary structure
  37. We can distinguish cases in which there are a defined number of copies of a single type of polypeptide chain (called a _______ or a _______) and cases in which there are defined numbers of each of more than one type of _____
    • subunits or a promoter
    • subunit
  38. In simple cases, the way in which the subunits associate does not change how the individual polypeptides _______. Often, however, the tertiary or even secondary structures of the components of a protein _______ depend on their association with each other. Explain and state an example
    • fold
    • oligomer
    • In other words, the individual subunits acquire secondary or tertiary structure only as they also acquire quaternary structure. One common example is the α helical coiled-coil: two (can 3 or 4) polypeptide chains, either identical or different, adopt α helical conformations and wrap very gently around each other. The chains are not as stable as a helices on their own and if the oligomeric interaction is lost, the separated helices unravel into disordered polypeptide chains
  39. Oligomer
    a protein composed of a small number of subunits
  40. The quatenary structure shown in class was made of ______ of the Nipah Virus (NiV F). It cannot work in _______ form
    • trimers
    • monomeric
  41. These structures can be represented in many forms including cartoon and cell surface digital representations. What is expected in each?
    • Cartoon: alpha helix, beta strands, the shape of the backbone, quatenary structure 
    • Cell surface: cell surface and side chains
  42. Polypeptide chains typically fold into one or more _______. Folding of a polypeptide chain creates an "inside" and an "outside" and thus generates _____ and ________ amino acid side chains respectively.
    • domains
    • buried and exposed
  43. If the polypeptide chain is too short, there are no _________ that bury enough _________ groups to stabilize a folded structure. If the chain is too long, the complexity of the folding process is likely to generate ______. As a result of these restrictions, most stably folded conformation include between about ____ and ______ amino acid residues.
    • conformations
    • hydrophobic
    • errors
    • 50 and 300 amino acid residues
  44. Longer polypeptide chains generally fold into discrete modules known as ______. Each of which generally within the ____ to _____ residue range just mentioned. The structures of individual domains of such a protein are similar to the structures of _____, ______-_____ proteins
    • domains
    • 50 to 300
    • small, single-domain proteins
  45. Each of the two or more domains of a folded polypeptide chain sometimes contains a ________ sequence of amino acid residues. Often however, at least one of the domains folds from two or more __________ segment(s) and the intervening part of the chain forms a distinct _______. The intervening domain then looks like an insertion into the domain that folds from the ________ segments
    • continuous
    • noncontiguous
    • domain 
    • flanking
  46. Classifications of protein domains allow simple, summary descriptions like the ones found in the CATH database. It starts with separation of proteins into classes according to their _______ structure. The most important levels in the classification hierarchy are ______ (aka ______) and _______.
    • secondary
    • fold aka topology
    • homology
  47. Name four ways CATH separates the proteins in to classes according to their principal secondary structures
    • by α helix
    • by β strand 
    • by a mixture of both
    • by a fourth class for the usually small domains with very little secondary structure
  48. The fold class  takes into account not only the _________ structures, but also how the chain passes from one ______ or _____ to another.
    • secondary
    • helix or strand
  49. A group of homologous proteins are ones with sequence similarities great enough to make what assumption?
    • Great enough to assume they have a common evolutionary origin 
    • **for very complex domains, a common origin seems intuitively reasonable
  50. What do short links between two domains of a folded protein allow vs long links?
    • short links allow a tight and rigid interface between them 
    • long link allow considerable flexibility
  51. Why do some proteins have extremely long flexible linkers?
    Because their function within a cell requires that the domains at either end interact over long and variable distances
  52. The amino acids for long linkers generally lack ______ ______ groups, which their extendable, flexible conformation cannot sequester from _____, and have other simplified features.
    • large hydrophibic groups
    • water
  53. When do amino acid side chains undergo modification? Name 4 such modifications
    • After the emergence of the polypeptide chain from a ribosome
    • acetylation, ubiquitination, phosphorylation and glycosylation
  54. The amino acid side chain modifications can modulate the _______ and ______ of a protein. One of the most important is _______. It is the addition of one or more ______ aka _______ to either an ______, ______ or _______ side chain.
    • structure and function
    • glycosylation 
    • sugars aka glycans
    • asparagine, serine or threonine side chain
  55. Glycosylation generally takes place in the _______ ________ of _______ cells, and is therefore a nearly universal characteristic of the ectodomains of ____-____ proteins and of ______ proteins.
    • endoplasmic reticulum 
    • eukaryotic cells
    • cell-surface proteins
    • secreted proteins
  56. Proteins bearing glycans are called _______. Enzymes that transfer glycans to asparagine side chains recognize a _____ ____ _____, Asn-X-Ser/Thr, where X can be any ______ ___ ____
    • glycoproteins 
    • short sequence motif
    • amino acid residue
  57. Phosphorylation of _______, _______, ________ or __________side chains is another widespread modification, critical for for _________ regulation. Phosphorylation of the _____ ______ residues occurs largely in eukaryotic cells; phosphorylation of the ______ is more common in prokaryotes
    • serine, threonine, tyrosine or histidine side chains
    • intracellular regulation
    • first three residues
    • last (residue)
  58. The folded or unfolded conformation of a protein under particular conditions is the one with the _______ free energy. If the environment of the protein changes, however, the most stable form can also ______. Name an example
    • lowest 
    • change
    • unfolding and refolding of ribonuclease in response to adding and removing a very high concentration of urea
  59. Changes in the environment of a protein can also induce functionally important, _______ shifts. For instance, when _______, is presented with its substrate, the single-domain hexokinase closes up around it
    • conformational changes
    • glucose
  60. Formation of energetically favorable contacts with the substrate makes the closed structure more _______ than the open one, shifting the position of the _______ _______ from mostly opened to mostly closed
    • stable 
    • dynamic equilibrium
  61. Interactions of two proteins with each other can cause one or both partners to undergo a ________ change. Sometimes, the interacting part of one of the partners is ______ (disordered and flexible) until it associates with the other partner. Explain.
    • conformational change
    • unstructured
    • The properly folded conformation is stable only in the presence of its target, which can be DNA or RNA as well as another protein.
  62. Both small molecules such as the ______ of an enzyme and macromolecules such as ______ and ______ ______ can make proteins undergo conformational changes.
    • substrates
    • proteins and nucleic acids
  63. Molecules that bind a protein or any other target in a defined way are called ______. ______ can regulate the activity of a protein (enzyme) by _________ a particular state. State an example
    • Ligands 
    • Ligands 
    • stabilizing
    • If binding of a ligand to an enzyme stabilizes a conformation in which the active site is blocked, the ligand will have turned off the activity of that enzyme
  64. The binding site for the inhibitory ligand doesn't have to _______ the active site, the binding ligand only needs to ______ the energy of a conformation in which the reactants cannot reach the _____ _____ or in which the _____ _____ no longer has the right configuration.
    • overlap 
    • lower
    • active site 
    • active site
  65. Allosteric regulation/allostery
    Ligand binding at a remote site favoring a conformation in which the active site is available to substrate and complementary to the transition state of the reaction; the ligand then becomes the activator
Author
chikeokjr
ID
331338
Card Set
The Structure of Proteins
Description
Ch 6
Updated