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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)
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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.
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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.
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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
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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
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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
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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
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Peptide bonds
covalent links between amino acids in a protein
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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
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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
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______, _____ 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
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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
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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
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How is the disulfide bond formed?
by oxidation of the two SH groups to S-S
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The resulting pair of amino acids, linked by the S-S covalent bridge, is sometimes called _______.
cystine
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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
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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)
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Water is an extensively ______ bonded liquid. Each water molecule can donate ____ ______ bonds and accept _____ _____ bonds.
- hydrogen
- two hydrogen
- two hydrogen
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The way in which a solute affects the hydrogen bonding of the surrounding water determines its ________ or _______ character.
hydrophilic or hydrophobic
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_______ 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
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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
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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
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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
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The remaining three levels depend on a protein's ______ _______ characteristics.
three dimensional
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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
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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
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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
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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
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In folded proteins, _____ ______ form sheets joined by ______ bonds in the _____ _____
- β strands
- hydrogen bonds
- main chain
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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
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In real proteins, various mixed sheets are often found rather either strictly _________ strand directions or strictly _________ ones.
- alternating
- unidirectional
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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
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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
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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
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Usually, the _________ of the secondary and tertiary structures of a polypeptide chain depend on each other.
stabilities
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Many proteins are composed of more than one polypeptide chain: _______ _______ refers to the way individual, folded chains associate with each other
quaternary structure
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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
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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
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Oligomer
a protein composed of a small number of subunits
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The quatenary structure shown in class was made of ______ of the Nipah Virus (NiV F). It cannot work in _______ form
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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
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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
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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
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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
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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
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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
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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
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The fold class takes into account not only the _________ structures, but also how the chain passes from one ______ or _____ to another.
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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
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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
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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
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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
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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
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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
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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
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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
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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)
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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
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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
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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
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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.
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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
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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
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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
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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
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