lectures 1-6 Flashcards
what are the methods of protein research
Protein crystallography, Cryo-electron microscopy, NMR spectroscopy
whats the weird amino acid that can fit into two categories
cystine
how do we determine the amino acid grouping from the amino acid
non polar has only hydrocarbons at their end of their sidechains or rings
polar uncharged: have an OH NH2 or O at end of the R side chain.
polar charged: tell by charge
what are the amino acid groups based off of
their charge state in an environment PH of 7
how do we name the amino acid residue mutations
First letter – original or native amino acid
- Number – location of mutation in the protein
- Second letter – new or mutated residue
for example E6V
define PKa
pKa value for an ionisable group on an amino
acid or protein is the pH at which the group is 50% ionised
define PI, isoelectric point
The pI, or isoelectric point is the pH at which the
net charge on an amino acid (or protein) is zero
what do we call amino acids once they are in a polpeptide
amino acid residues or residues
whats a post-translational modification
A chemical group can added to an amino acid residue after translation has occurred → PTM!
how are PTMs added
Added via covalent attachment (usually enzyme-mediated)
what do PTMs do
Modify the protein is a way that switches it on or off, directs cellular
location, targets for degradation etc
what type of reaction is the formation of a peptide bond
a dehydration or condensation
what does it mean to be a globular protein?
a protein which is roughly circular in shape
define secondary structure
The three-dimensional arrangement of a protein chain over a short stretch of adjacent amino acid residues. Includes -helices and -sheets
whats the phi bond?
the bond between the alpha C and the N
whats the psi bond
the bond between the alpha C and the carbonyl carbon
what values can the phi and psi bonds take on
anywhere from 0 to +-180 degrees
whats the omega bond and what values can it take on
the peptide bond is the omega bond, it is either 0 or 180 degrees
can phi and psi be any value at any point?
no they cannot, they have limited accessible values due to steric hindrance
over phi and psi rotation can lead to what
over phi can lead to O-O collisions
over Psi can lead to NH-NH
whats peptide bonds are what and whats the bond angle for this
most are trans at 180 degree rotation
what the value of rotation for cis peptide bonds
0 degrees
beta strand vs beta sheet
a beta sheet is a collection of beta strands
what are alpha helices stabilised by and where are they
stabilised between H bonds at N and N+4
what are the key features of the alpha helix
3.6 residues, right handed turn, side chains point out from the centre, don’t have glycine and proline in them as they interupt the helix, altnerates between polar and non polar side chains
key features of the beta sheet
2-10 strands per sheet, stabilised between hydrogen bonds, each strand approximately 6-15 residues long, the side chains alternate between point up and pointing down,
in alpha helix each amino acid is separated by how much
100 degrees turn
describe antiparallel beta sheets
Strands run in the opposite direction.
Hydrogen bonding pattern is optimal. usually a turn between each strand
describe parallel beta sheets
Strands run in the same direction, less optimal H bonds, usually an alpha helix between each stand, or a loop/coil
key features of turns
involve 3-4 residues, lots of glycine and proline, type 1 and type 2 very common
why is glycine good for turns
Small side chains make glycine very
flexible. It has a lot of conformational
freedom.
why is proline good for turns
Proline is too rigid for helices but has
a built-in turn because of the bonding
between the R-group and the amino
group.
what is super secondary structure?
helices and beta strands connected by loops or turns to make local regions of secondary structures
what is a domain
independently folded regions that often
possess a specific function within the
protein.
what makes up domains
super secondary structures combine to form domains and the domain has a hydrophobic core normally.
proteins can be grouped into families based on what? examples please
s based on tertiary
structure – three examples…
alpha domain family
alpha/beta family
antiparallel beta family
combinations of what can be used to make different functioning proteins
combinations of different domains
what drives protein folding
the sequence of amino acids more specifically the hydrophobic amino acids
who was the guy who solved protein folding and what was his test
The Anfinsen Experiment. he took a protein and denatured it with urea and mercaptoethanol. he then removed these things and then the protein folded back to exactly how it was before. showing that the information to fold is in the amino acid sequence it self
whats the likely sequence of events for protein folding
(i) Formation of short secondary structure segments
(ii) Subdomains form
(iii) Subdomains come together to form a partly
folded domain; a “molten globule” that can rearrange,
(tertiary structure still partly disordered)
(iv) Final domain structure emerges, small
conformational adjustments to give final compact
native structure
whats the most important contributor to protein stability
The hydrophobic core
what are some common super secondary structures
beta hairpin, greek key, helix-turn-helix, EF hand proteins
what collectively makes strong contribution to the conformational stability of protein
non covalent interactions
what are the non-covalent interactions in proteins
metal ion coordination, hydrophobic interactions, electrostatic attraction,
what covalent bond can proteins do
disulphite bridges
whats an aggregate
when proteins fold improperly and the hydrophobic regions bind to hydrophobic regions of another protein to form a mishapen protein aggregate
what are chaperones
Sometimes the protein may not fold itself completely correctly. Chaperones can be used. these are proteins which help the protein to fold correctly and not form aggregates
what are the 3 folding methods of proteins
Chaperone-independent
b) Chaperone-dependent e.g.,
Hsp70
c) Chaperonin-dependent e.g.,
GroEL-GroES
different between chaperone and chaperonin
chaperonins which are like a bin, they insert the protein making a favourable environment for folding on the interior of the chaperonin. chaperones fold the protein sequence whilst still in solution
what are prions
prion is a misfolded protein that can transmit its misfoldedness to normal variants of the same protein and trigger cellular death. these prions form aggregates with other proteins, inducing them to become prions
examples of prion related disease
mad cow disease, alzheimers
