Chapter 6: 3D Structure of Proteins Flashcards
What was the first protein to be sequenced and who sequenced it?
Insulin and Sanger
is protein structure generally still planar and trans?
yes.
Peptide bond (amide bond) still causes the chain to be planar (because it still can’t rotate) and trans configuration is still thermodynamically/sterically favorable. (so it’s more often found in nature)
what does a Ramachandran plot show you?
The thermodynamic favorability of all possible psi and phi angles for a given alpha carbon in a protein
what does the ‘L’ space on a Ramachandran plot show you?
the configuration where most L amino acids appear
what does a little ‘alpha’ symbolize on a Ramachandran plot?
The configuration from which alpha helices arise
what does a little up and down arrow symbolize on a Ramachandran?
The configuration from which beta sheets arise
where is the ‘L’ space on a Ramachandran plot?
On the left hand side of the plot
where is the ‘D’ space on a Ramachandran plot?
On the right hand side of the plot
which axis shows you the phi angle on a Ramachandran plot?
x axis
which axis shows you the psi angle on a Ramachandran plot?
y axis
why does the Ramchandran plot have so many configuration possibilities for glycine?
because glycine (being achiral) is neither L nor D and has no hindering side chain
in 1951, What did Linus Pauling and Robert Corey both simultaneously propose about proteins’ secondary structure?
- the structure is sterically allowed & favorable (according to Ramachandran plot)
- the structure maximized H bonds between the protein backbone’s amide and carbonyl groups
which amine and carbonyls (in a protein chain) participate in hydrogen bonding when the protein is in its 2o structure?
all of them!
how many residues does it take for a protein chain to turn over on itself IN A HAIRPIN TURN?
exactly 4 amino acids
what does the term ‘pitch’ describe in reference to a protein with alpha helix structure?
the distance the helix rises per turn
= 5.4 Angstroms
Do L amino acids have right handed alpha helix or left handed alpha helix?
right
in an alpha helix, which amino acid is the ‘i’ acid hydrogen bonded to?
i + 4
in an alpha helix, which way to the side chains point (in/towards the core or out/away from the core)
out
in an alpha helix, what are the 2 reasons (r/t size and H bonding) why the side chains point out/away from the core?
- this minimizes steric hinderance
2. maximizes hydrogen bonding between the amine and carbonyls in the back bone
which amino acids are more likely to result in an alpha helix structure: large or small amino acids?
small ones; because they have less steric hinderance
which two amino acids rarely result in alpha helices, even though they are small?
glycine and proline (of course); they typically form hair pin turns instead
why don’t glycine and proline typically form alpha helices?
They have too many thermodynamically favorable bond angle combos to be constricted to the helix shape
why does proline especially not form alpha helices all that often?
The ring won’t conform to the needed angles.
It will cause a kink in the protein if it tries
which structure is drawn as a helical wheel when viewed from a bird’s eye view: alpha helix or beta sheet?
alpha helix
what factors may help to give the alpha helix its stability?
charges/polarity of the side chains
do side chains in an alpha helix attract/repel each other up and down or around and around?
up and down
what are the other 2 types of helices besides alpha?
3_10 and pi
how can you tell when a protein will adopt a helix shape rather than a pleated shape?
if the protein has a bunch of small/unhindered side chains, it will likely form alpha helix.
If the protein has a bunch of large/bulky/hindered side chains, it will likely form a pleated sheet
why do proteins with bulky side chains favor the pleated sheet shape?
this shape helps to keep the bulky side chains further apart/reduces steric hinderance
what are the 2 types of pleated sheets?
parallel and anti parallel
what is the structural difference between parallel pleated sheets and antiparallel pleated sheets?
in parallel pleated sheets, the hydrogen donors and acceptors are directly parallel to one another (because the sheets are side by side?)
In antiparallel pleated sheets, the hydrogen donors and acceptors are to an angle of one another
what is a beta barrel?
what you call it when a pleated sheet rolls over onto itself like a big tube
what was the point of us talking about jelly fish protein in class?
the jelly fish protein GFB is a beta barrel protein and its fluorescence has been transferred to other animals and proteins making them glow in the dark.
Makes targeted proteins more trackable
are hair pin turns/loops more common in parallel beta sheets or antiparallel beta sheets?
antiparallel
why are hair pins turns so common?
given that they only require 4 amino acids, they are the fastest/most efficient turn
why is glycine so common (especially in the 3rd position) of hair pin turns?
since it’s achiral, it can readily adopt the D-like character that is advantageous for more efficient turns needed for turns?!!!
what is a random coil turn/loop?
what you call a 2o protein structure that DOES NOT have a defined shape and can’t be described by a term like alpha helix or beta sheet
like an uncooked spaghetti; can’t been examined easily using conventional methods because it’s not ordered enough to be detected.
What is a coil structure?
what you call a 2o protein structure that has a DEFINED shape but can’t easily be described by another term (e.g. alpha helix or beta sheet)
what is a hair pin turn/loop?
a section of a protein where the structure changes direction in 4 amino acids.
what 3 factors increase the likelihood that an alpha helix will form rather than a beta sheet?
- presence of small side chains; no bulk or beta branches near the back bone
- presence of polar side chains
- absence of side chains whose charges repel each other
What are the four ways of describing protein structure?
primary, secondary, tertiary, quaternary
What does the primary structure of protein show you?
The sequence of amino acids in their correct order, linked by peptide bonds
What does the secondary structure of protein show you?
the local interactions between a protein’s primary structure
What does the tertiary structure of protein show you?
long range interactions between units of the protein’s secondary structure
What does the quaternary structure of protein show you?
3d structure of a protein composed of MORE THAN ONE folded protein
which carbon is the alpha carbon in an amino acid?
The one with the R group
what is the significance of psi and phi bonds in an amino acid compared to peptide/amide bonds?
psi and phi bonds can rotate freely but peptide bonds cannot.
which angle (psi or phi) is between an amino acid alpha carbon and its carbonyl?
psi
which angle (psi of phi) is between an amino acid alpha carbon and its amine?
phi
what does it mean to say that a phi or psi angle is a dihedral (torsion) angle?
It means you are referring to an angle between two intersecting planes or half-planes.
In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common.
True or false: all dihedral angles are possible (but some are more favorable than others)
true
what drives a lot of the shape of 2o structure?
hydrogen bonding
How did Pauling develop his ideas about the way a 2o protein structure is shaped?
through drawing structures
How did Corey develop his ideas about the way a 2o protein structure is shaped?
through experimental practices
what are the psi and phi angles for all alpha helices?
the psi angles are all -47 degrees (on average)
the phi angles are all -57 degrees (on average)
what the pitch for all alpha helices (in Angstroms)?
5.4 angstroms
what is the hydrogen bonding pattern (in terms of the ‘i’ convention) for all alpha helices?
the carbonyl in the i position is hydrogen bonded to the amine in the i + 4 position
what is the hydrogen bond distance for all alpha helices?
each hydrogen bond is 2.8
in a helical wheel, which two amino acids are closest in space and often bound via ionic or hydrophobic interactions?
i and i+3
what 4-ish amino acid conditions are ideal for forming alpha helix? Dr. Shimko calls these ‘rules’ for alpha helices.
- amino acids should be small
- amino acids should not have beta branches
- amino acids’ charges/polarity cannot be unpaired/unmatched
- glycine and proline cannot be included
which is more favorable: parallel pleated sheets or antiparallel pleated sheets?
antiparallel
do parallel pleated sheets and antiparallel pleated sheets have the same phi and psi bond angles?
No
which type of pleated sheet has linear hydrogen bonds: parallel or antiparallel?
anti parallel pleated sheets
which type of pleated sheet has NON-linear hydrogen bonds: parallel or antiparallel?
parallel pleated sheets
Do you still need to draw your amino acids from the N terminus to the C terminus?
Yes! Make sure you draw an arrow if you need to show which end is which/what direction your amino acid chain is pointed in
what color is usually used for the nitrogen in a ball and stick model for amino acid?
blue
what color is usually used for the oxygen (in the carbonyl) in a ball and stick model for amino acid?
red
where are the side chains relative to the backbone in a pleated sheet?
above and below the sheet
what 2 factors increase the likelihood that a beta sheet will form rather than an alpha helix?
- large side chains
2. bulky (beta branched) side chains
can you have antiparallel pleated sheets in the same protein as parallel pleated sheets?
yes
what role does hydrophilicity/hydrophobicity play in the shape of a beta barrel protein?
the hydrophilic r groups will be above the sheet/facing up and out towards the aqueous environment and the hydrophobic r groups will be below the sheet/facing inside the aqueous environment.
why are the beta hair pin turns’ psi and phi angles irregular?
their angles have to be pretty constrained in order to facilitate the most efficient turn possible
What are the 2 types of beta hair pin turns?
Type 1: L.L. hair pin turns
Type 2: L.D. hair pin turns
how can you tell the difference between a Type 1 LL hair pin turn and a Type 2 LD hair pin turn)?
compare the phi and psi angles in the turns’ SECOND AND THIRD amino acids:
In Type 1: all angles in question will be allowable/favorable for L amino acids
In Type 2: the 2nd amino acid’s angles will allowable/favorable for L but the 3rd amino acid’s angles will be allowable/favorable for D
can alanine work as well as glycine in the 3rd position of a hair pin turn?
no.
it’s less favorable than glycine, but will get the job done if it means improving favorability of other interactions elsewhere in the protein.
can alanine be used in place of glycine in the 3rd position of a hair pin turn?
yes…but it’s less favorable
It will be tolerated in the 3rd hair pin position if it means improving favorability of other interactions elsewhere in the protein.
Along with glycine (and sometimes alanine), why is proline commonly found in hair pin turns?
because it can adopt a (round/c-shaped) cis amide bond, which facilitates the turn in the hair pin turn.
Proline’s participation in hair pin turns has nothing to do with its psi and phi bond angles.
when proline is found in a hair pin turn, does it have to appear in the 3rd position (like how glycine and alanine do)?
No.
As long as the proline has ‘a cis amide N terminal, it can help facilitate the turn in the hair pin.
What does ‘desolvation cost’ refer to?
The energy it costs of breaking existing hydrogen bonds (between water and unfolded protein) in order to create new hydrogen bonds (between the amides and carbonyls in the protein backbone)
Generally, this net cost is 0 (and that’s why hydrophobic effect is credited with triggering protein folding rather than entropy).
What is it about the hydrophobic effect that makes it a bigger facilitator of protein folding than just entropy?
Hydrophobic effect is driven by effort to release caged water. Release of caged water has a huge impact on the entropy of the system as a whole; much bigger than whatever energy reduction is achieved by having the protein stop H bond to water in order to H bond to itself.
Why isn’t H bonding considered to be the CAUSE of protein folding?
The delta G is produces is essentially 0
What are the 3 types of tertiary protein structure INTERACTIONS Dr. Shimko went over in class?
Disulfide bonds
Hydrogen bonds
Ion pairs (salt bridges)
The other ones are:
hydrophobic interactions (mostly between R groups)
Pi pi stacking (overlap of aromatic groups)
What amino acid (residue) gives rise to disulfide bonding in secondary and tertiary protein structure?
Cysteine. They sulfurs bind to create disulfide bonds.
How can you tell if a tertiary interaction is a H bond or an ionic bond/salt bridge?
The H bond will involve partial charges.
The ionic bond/salt bridge will involve full fledged charges.
what does it mean to say that an amino acid has a beta branch?
it means that the beta branch has TWO non-hydrogen atoms connected to the beta carbon
which 3 amino acids have beta branches (and should thus be excluded from alpha helices)?
Valine
Isoleucine
Threonine
