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MCB 2000. Exam 1 (Protein Structure)
Terms in this set (22)
how do we go from a lined structure to a folded structure?
why is form fits function appropriate in protein folding?
if a protein's structure is incorrect, its function will no be what it should be --> could lead to disease
when oxygen binds to hb, what kind of bonds are changed?
the non covalent interactions are being disrupted.
Hydrogen bonds are affected, this is why the conformation switches.
characteristics of the levels of protein structure: primary
the linear sequence of amino acids. this is what the ribosome would read
characteristics of the levels of protein structure: secondary
-what type of bonding stabilizes secondary structure?
-which parts of the amino acid sequence are involved in binding?
-describe the rate of folding? is it a fast/slow process?
-involves H bonding along the polypeptide backbone
-H bonding stabilizes secondary structure
-does NOT involve the side chains
-folding happens immediately. while the ribosome is still working on other parts of the protein, the other parts are being folded simultaneously
characteristics of the levels of protein structure: tertiary
-this level comes as a result of side chain interactions
-now we see different types of bonds like ionic, hydrophobic interactions and disulfide bonds forming at this level
characteristics of the levels of protein structure: quaternary
-what is the difference between quaternary structure and tertiary structure?
-what types of bonds are common at this level?
this structure is basically just 2 or more polypeptide chains interacting together
-pi bonds and ionic bonds here are common
how many types of secondary structure are there?
beta sheet and
which two types of secondary structures are repetitive?
alpha helix and beta sheet
characteristics of the alpha helix:
what stabilizes the alpha helix structure?
describe what the a helix looks like in cartoon form? and in regular form.
what does the bonding look like in depth?
what is the general shape of the a helix?
which direction do the side chains point? what types of interactions are they having?
how are the psi and the phi angles related? and how is this relation shown?
-H bonding is the stabilizer
-in cartoon form, it looks like a rotini noodle. or a slinky
-in regular form, the amino group of one amino acid and the carbonyl group of the other amino acid are bonded together. these two groups are 4 positions away from each other.
-the general shape is a cylindrical structure
-the side chains are pointing outward but they are NOT interacting
-the psi and phi angles are similar and more limited. you can tell that the angles are similar because of the consistent shape of the helix
describe the steric constraints on the alpha helix.
-which amino acids are less common in an alpha helix? (they must be strategically placed)
it's less likely that you'll see two aliphatic groups next to each other or a really bulky side group next to each other because of the steric hindrance that might take place.
ex. amino acids like valine, isoleucine and threonine are less common because of their long side chains
in regards to reactivity, which amino acids are less likely to form in an alpha helix?
serine, aspartic acid, asparagine
because their side chains are hydrogen bond donors/acceptors that compete with the main chain of H bonds in the polypeptide backbone
describe how proline fits into the alpha helix. how is it a constrain on the helix? why wouldn't you see it in a helix very often? same with glycine
why is proline called a helix breaker?
how is glycine a constraint on the helix?
proline has a unique ring structure and because of it, it cannot fully participate in the helix. it's psi angle is not consistent with the helix and because of that, proline is often called a helix breaker because you usually see it at the end of the helix where the structure is about to change out of a helix
you wouldn't see it because it would introduce a bend in the helix and you wouldn't find glycine because it is too small
glycine is a constraint because the H side chain allows for unconstrained rotation and this destabilizes the helix (makes it less rigid)
what is the difference between a beta strand and an alpha helix?
how is a beta strand different than an alpha helix in regards to bulky R groups?
how do the side chains extend on a beta strand compared to an a helix?
an alpha helix is a compact structure but a beta strand is a more extended structure.
since a beta strand is more extended than an alpha helix, it is more accommodating for bulky side chains
the side chains on an beta strand extend above and below the plane as opposed to inside and outside the helix
how is a beta sheet formed? what types of interactions are involved?
a beta sheet is formed by H bonding between backbone atoms on different beta strands.
-no side chains are interacting so many different sequences can form a beta sheet
what does a beta sheet look like in cartoon form?
is directionality significant?
it is usually depicted as a series of flattened arrows.
the arrows provide directionality. they point toward each strands carboxy terminus
why is it significant that the side chains in a beta sheet extend above and below the sheet?
this allows for the different sides of the strand to have different properties
when the beta strands are interacting in a parallel fashion, are the H bonds perpendicular or slanted?
and what about when the beta strands are interacting in an anti-parallel fashion?
when beta strands are antiparallel= H bonds are perpendicular
when beta strands are parallel= H bonds are slanted
((try to think of that picture))
what is the purpose of beta turns?
-in one strand?
-between many strands?
-are the repetitive or non repetitive structures?
-how many amino acids participate in the beta turn structure?
-they allow for a change in direction of a protein
-they can connect many strands of proteins
-they are non repetitive structures
-4 amino acids participate in the beta turn structure
tertiary structure involves what type of interactions between what parts of the amino acids?
they involve non covalent interactions between the side chains of amino acids.
tertiary structure is where we see amino acids that are far apart in primary structure brought closer and interacting via non covalent bonds
at which structure levels do domains exist? and what is a domain?
do domains have to have a specific secondary structure?
domains exist on the tertiary level
domains are ways for certain regions of a polypeptide chain to be identified. say theres a part of the polypeptide chain that interacts with atp, that is its own domain.
domains do not have to have a specific secondary structure. you could shave domains on an alpha helix or a beta sheet
how can you identify quaternary structure?
-how can you tell the difference between tertiary structure and quaternary structure?
(what's the strategy?)
when you see two or more polypeptide chains
ex. hb contains of 4 polypeptide chains (2 alpha subunits and 2 beta subunits)
-quaternary structures have more than 1 subunit
-if you find the number of termini, and there is more than one of each termini, then it is quaternary structure
ex. since hb has 4 polypeptide chains, it will have 4 amino termini and 4 carboxyl termini
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