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chapter 6: proteins-three-dimensional structure
Terms in this set (144)
what bond is responsible for joining two amino acid residues together?
with respect to atoms, what conformation is the lowest in energy?
why is the cis conformation less stable than the trans conformation?
there is steric interference between neighboring side chains
this refers to the atoms that participate in peptide bonds, ignoring the side chains
this is composed of a series of rigid planar peptide groups (backbone)
the conformation of the backbone can be described by what?
what is the C-N bond called?
what is the C-C bond called?
what does the blue area of the Ramachandran Diagram represent?
sterically allowed conformation for all residues
what does the green area of the Ramachadran Diagram represent?
the outer limit of acceptable areas
(possible but unlikely)
what does the yellow area of the Ramachadran Diagram represent?
the most common secondary structures
why are some things called regular secondary structures?
they have repeating phi and psi values
how are secondary structures of proteins formed?
from hydrogen bonding between the amide hydrogen and carbonyl oxygen on separate residues
these from hydrogen bonding between the amide hydrogen and carbonyl oxygen on separate residues
by systematically varying phi and psi, a plot can be determined which show the stable conformations
because the conformation freedom is strained, what else is strained?
the alpha helix is a _____ handed helix.
how are the hydrogen bonds on the alpha helix?
(almost perfect length)
what does it mean for an alpha helix to avoid steric interference with each other and with the backbone?
the amino acid side chains are arranged on the outside of the helix and point down
what happens when the amino acid side chains are arranged on the outside of the alpha helix and point down?
steric interference with each other and the backbone is interfered with
where does the beta sheet occur?
between neighboring polypeptide chains
what keeps the beta sheets together?
(between the N-H and C double bonded to O groups)
what helps reduce steric hindrance on beta sheets?
side chains of a polypeptide chain extend to opposite sides of the sheet
the side chains alternate R-groups
this occurs when the neighboring polypeptide chains run in opposite directions (beta sheets)
antiparallel beta sheets
describe the hydrogen bonds of the antiparallel beta sheet.
the hydrogen bonds form nicely and are not distorted !
this occurs when the neighboring polypeptide chains run in the same direction of beta sheets
parallel beta sheets
why are parallel beta sheets less stable than antiparallel?
the hydrogen bonds are distorted.
describe the hydrogen bonds of parallel beta sheets.
they are not straight across, and this makes them weaker
about how many strands do parallel beta sheets need to have?
at least 5!
how do beta sheets normally occur?
with a mixture of parallel and antiparallel strands
what kind of twists are seen in the beta sheet?
a right handed twist
why do beta sheets see right handed turns?
DUE TO the interactions between residues
what does the twist of the beta sheet form?
forms as a compromise between optimizing the conformational energies of its polypeptide chains and preserving its hydrogen bonds
this weakens the hydrogen bonds BUT tries to minimize R group repulsions
what can the connection between two beta sheets be?
what size of loop does an antiparallel sheet have?
what size of loop does a parallel sheet have?
these are irregular protein structures
these contain long stretches of regular secondary structure
(alpha keratin and collagen)
what role do fibrous proteins have in living organisms?
what occurs in all higher vertebrates?
what does alpha Keratin form? (structure)
what kind of a twist does a coiled coil do?
describe how the coiled coils form?
• each individual chain is an alpha helix
• two alpha helices are wrapped around each other
what residues line up in the coiled coil?
a & d,
this forms a hydrophobic strip
what helps facilitate the assembly of the coiled coils into protofilaments?
N- and C- terminals of each polypeptide
what does two protofilaments form?
what do four protofibrils form?
what is alpha keratin rich in ?
what do the cysteine residues of keratin tell us?
the number of disulfide bonds (which form between the cysteine residues), the stronger the alpha keratin will be
describe how perms work.
• ammonium thioglycolate reduces the disulfide linkages by oxidizing them
• the hair is placed in the formation it wants to be in
• hydrogen peroxide reoxidizes to reform the disulfide linkages
• the forming of the hair changes where the disulfide bonds are placed, changes hair shape
what is the structure of collagen?
a triple helix
where does collagen exist?
in all multicellular animals
this exists in all multicellular animals
what is about 1/3 of collagen's residues? And its other makeups?
-another 15-30% is Proline (Pro) and proline derivatives (4-hydroxyprolyl)
how are proline residues converted to 4-hydroxyprolyl residues?
in a reaction catalyzed by prolyl hydroxylase
requires ascorbic acid (vitamin C) to maintain its activity
why does scurvy happen?
due to a deficiency in vitamin C
• collagen will not form properly
what are the amino acid sequences of a typical collagen polypeptide?
• X = Proline
• Y = 4-hydroxyprolyl
what does proline do in the collagen structure?
• prevents the formation of an alpha helix because it cannot form the backbone conformation
• it also does not have the N-H group to hydrogen bond
where does each third residue of the polypeptide chain go in collagen?
passes through the center of the helix
what residue is needed to be the third residue in collagen?
glycine, it is the smallest (since it will pass through the center of the helix)
how are the peptide bonds of collagen oriented?
the N-H of each Gly makes a strong hydrogen bond with the carbonyl oxygen of an X (Proline) residue on a neighboring chain
why is the assembly of collagen so rigid?
because Pro and Hyp are bulky and inflexible
why is collagen such a strong protein?
the polypeptide chains are twisted in opposite directions
why is collagen covalently cross-linked?
very few cys residues are present so disulfide bonds are not possible
what cross-links Lys and His residues in collagen?
describe the cross links that occur in collagen...
• the cross-links are not random
• they occur near the N- and C- terminals of collagen
•the degree of cross-linking increases with age
(babies taste better, the meat from older animals is tougher)
these have no apparent order in terms of amino acid configurations
describe random coils
• they have random values for the phi and psi bonds from one amino acid to the next
• these regions form a stable confirmation
what can distort the regular secondary structural elements?
variations in amino acid sequences
this directly images molecules by looking at the electron density
what are the covalent bond distances and the wavelengths of X-rays?
what does the darkness of a spot relate to on x-ray crystallography?
where can the shape of a polypeptide backbone do?
be traced and side chain orientation and position can be determined
how can side chain orientation and position of a protein be determined?
by looking at the distinctive shape of a polypeptide
how are the side chains of proteins oriented?
based on their polarities
• nonpolar residues tend to occur in the protein interior
• polar residues tend to be on the exterior
where are nonpolar residues in the side chain of a protein?
on the inside
where are polar resides in the side chain of a protein?
on the outside
where can the uncharged polar side chain residues be on the protein?
• often occur on the exterior
• *IF they are in the INterior, they can hydrogen bond
these are globular protein's tertiary structure that consists of secondary structural elements that combine to form
• (supersecondary structures)
this motif consists of two parallel strands of a beta sheet connected by an alpha helix
this motif consists of antiparallel beta sheets connected by relatively tight reverse turns
beta hairpin motif
this motif consists of two successive antiparallel alpha helices packed against each other with their axes inclined
alpha alpha motif
this motif consists of a beta hairpin being folded over to form a 4-stranded antiparallel beta sheet
Greek key motif
how are proteins classified?
BASED ON THE TYPES OF SECONDARY STRUCTURE THEY CONTAIN
proteins that only contain alpha helices
what depict alpha helices?
how are proteins identified?
by the color of the rainbow
proteins that consist of only beta sheets?
what proteins are alpha proteins
what proteins are beta proteins?
proteins that contain alpha helices and beta sheets
what proteins are alpha/beta proteins
-also lactate dehydrogenase
a way to classify proteins based on how their secondary structures are connected
extended beta sheets often roll to form
describe the structure of beta barrels
• hollow in center
•can bind/let things pass
• multiple beta hairpin motifs
this consists of overlapping beta-alpha-beta motifs
large polypeptides (>200 residues) generally form into two or more clusters known as
what happens in between domains?
a cleft forms
• allows for small molecules to bind
what do domains often have?
a specific function
domains that persist do what?
• are stable
• can tolerate additions/deletions
• support life function
what is the most important part of the protein and why?
the STRUCTURE because it determines how the protein will interact
the study of biological information in the form of molecular sequences and structures
in their quaternary structure, what do many proteins function as?
non-covalent associations of several identical proteins
•some function as associations of two or more different proteins held together by non-covalent interactions
proteins with more than one subunit
identical units of oligomers
how many subunits does hemoglobin consist of?
(two sets of two)
in quaternary structure, when multiple copies of the same protein associate, they must form what?
a symmetrical aggregation
why can quaternary structure proteins not have mirror images?
most amino acids are L, if they are flipped like they are in their mirror image, they would turn into D
what is the main force that keeps proteins together?
the hydrophobic effect
protein stability depends primarily on hydrophobic effects and secondarily on electrostatic interactions
why is the aggregation of nonpolar side chains internally favored?
there is an increase in entropy
these express the hydrophobic and hydrophilic tendencies of amino acids to be inside or outside of a protein
the greater this, the more likely a residue will be inside a protein
what does a higher hydropathy mean?
the more likely a residue will appear inside a protein
away from aqueous solvent
how does one determine hydropathies?
can have the primary structure, add up the hydropathy ratios
how much do hydrogen bonds help the proteins?
they dont really do much
•in unfolded proteins, residues can hydrogen bond to water
• if a protein folded in a way that prevented a hydrogen bond from forming, that would be very unfavorable
ionic groups of opposite charge can form
how much do salt bridges contribute to the stability of proteins?
not a lot
•DUE TO loss of entropy and loss of solvation free energy
•salt bridges lock the protein in place, so they cannot move, the entropy decreases
when do disulfide bonds occur?
as a protein folds
(to its native conformation)
at least ten motifs are nucleic acid binding proteins
describe zinc fingers
• short peptide chains because of the zinc
• they can do chains (otherwise they would not form)
•zinc only has one oxidation state, so the fingers will remain like how they are
a loss of structure
heatt causes the entire peptide to unfold
cooperatively (at the same time)
what can pH variations do to denature a protein?
alter the ionization states of amino acids and disrupt salt bridges and hydrogen bonds
what can detergents do to denature a protein?
they associate with the nonpolar residues of a protein and interfere with the hydrophobic interactions
•ampiphile (reduce hydrophobic effect ((protein folding)))
what can chaotropic agents do to denature a protein?
they increase the solubility of nonpolar residues in water
(guanidinium ion, urea)
•if nonpolar residues become soluble, the hydrophobic interactions of proteins can also unfold
what can renature a protein after denaturation?
what does renaturation imply?
a protein/s primary structure dictates its 3D structure
1. everything is denatured and cleaved
2. removal of the denaturant and reductant allows the protein to renature and reform disulfide bonds in the presence of oxygen
3. removal of only the mercaptoethanol allows the disulfide bonds to reform
4. subsequent removal of the urea generates an enzymatically inactive protein in which the disulfide bonds have formed at random
5. adding a small amount of mercaptoethanol to the scrambled protein in the absence of O2 catalyzes its conversion to the active enzyme through disulfide interchange reactions that allow the native disulfide bonds to form
proteins are dynamic so this means..
protein structures are flexible and may include unfolded regions
•conformational changes can favor one conformation over another
• if all amino acids "tried" every allowable conformation, it would take a very long time for it to fold
aggregation of hydrophobic groups
• allows for secondary structure to occur quickly
a species which has much of the secondary structure but little of the tertiary structure of the native protein
the relationship that a folding protein follows - a pathway from high energy and high entropy to low energy and low entropy
what do the clefts and gullies of a folding funnel represent?
conformations that are temporarily trapped until they overcome an energy barrier through random thermal motion
what is a driving force to protein folding?
why is entropy not a driving force to protein folding?
as a protein folds, it gets more ordered, and it has less and less entropy
where do proteins fold slower?
in vitro (in test tubes)
what catalyzes disulfide bond formation?
protein disulfide isomerase (PDI)
these assist protein folding via an ATP-dependent bind-and-release mechanism
how do the molecular chaperones work?
they bind to unfolded and partially folded polypeptide chains to prevent the improper association of exposed hydrophobic segments
•this helps to prevent nonnative folding as well as aggregation and precipitation
•also induce misfolded proteins to refold to their native conformation
ESPECIALLY IMPORTANT FOR MULTIDOMAIN AND MULTISUBUNIT PROTEINS WHOSE COMPONENTS MUST FOLD BEFORE THEY CAN PROPERLY ASSOCIATE WITH EACH OTHER
what diseases result from protein misfolding?
(result in aggregates)
PRECIPITATES IN THE BRAIn
what happens in alzheimer's?
a neurodegenerative disease that is characterized by the formation of amyloid plaques
•these plaques consist mostly of a protein named amyloid-beta-protein, that is a protein of a larger fragment
(part that was deposited into solution is hydrophobic)
proteins that are able to infect other proteins
describe amyloid fibrils
the misfolded proteins form fibrils containing extensive beta structure
•the beta strands are oriented perpendicular to the fiber axis
• ALL of the misfolded ones will, when it refolds, associated with a larger complex of refolded proteins and then it falls out of solution due to solubility
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