protein structure Flashcards
what are the four groups present in a amino acid?
> be specific about their properties
amino = acid so proton donor
carboxyl = base so proton acceptor
R side group = this is variable so can change
Hydrogen
what does chiral mean?
it cannot be superimposed (mirror image)
each vairent is called an enanitomers
what is a zwitterion?
dipolar ion with 0 charge
only exisits at the isoelectric point at which pH is 7
where the amino acid is protonated
SIDE CHAINS
Gly
Ala
Ser
Hydrogen
CH3 = methyl
CH2OH = some polarity due to electronegative Oxygen
SIDE CHAINS
Cys
His
CH2SH
aromatic ring = potentially be acharged molecule
whats the difference between an aa and amino residue
residue does not have a free amino/carboxyl group
but esentially the same thing
what is cool about double bonds?
they cannot rotate
are sidechain interaction involved in secondary structures of proteins?
NO. it only involves the backbone
facts about ALPHA HELIX
> held by hydrogen bonding
right handed helix (so turns towards the right)
side chains project out at 100° so have 3.6 residues a turn
n to n+4 linkage so Carboxyl2 to amine6
it can stretch ———– longitudinally
but it is rigid | laterally
> like a slinky
why is Proline /P considered a helix breaker?
it cannot rotate as its sidechain is connected to its amino group (loop)
irregular geometry interrupting the backbone
why is Tyrosine/Y considered a helix destabiliser?
it has a large bulky side group
common aa found to create alpha helix
Alanine Arginine Histidine Leucine Lycine Glutamate Glutamine
facts about beta sheets
can be parallel or antiparallel
> anti parallel is flexible laterally but NOT longituidnally as its already extended
Amino acids can have two isomeric forms, L or D. Which form(s) is found as constituents of proteins?
A L-isomer
B D- isomer
C Both isomers
YAAAY Only L isomers can form proteins
What are the key features of an alpha-helix?
> but drill it into your mind!
Right-handed
3.6 residues/turn
n to n+4 linkage
Side chains project out at 100° to each other
What is the difference between parallel and anti-parallel beta sheets?
parallel has weaker hydrogen bonding and had R groups that are available to interact
What makes an amino acid a zwitterion?
A No charges on any atom
B Negative charge on amino group only
C Positive charge on carboxyl group and negative charge on amino group
D Positive charge on amino group and negative charge on carboxyl group
OPTION D
In solution under neutral conditions, an amino acid residue will exist as a dipolar zwitterion. The COOH looses the H to from COO-, and the NH2 gains the H+ to form NH3+.
What method of purification of proteins involves the unfolding of a protein by coating it with a detergent? A Size Exclusion Chromatography B Affinity Chromatography C Precipitation by ammonium sulphate D Isoelectric focusing E SDS-PAGE
OPTION E
> charged and hydrophobiC which allows protein to be dragged through gel
> smaller protein moves faster
> protein can be stained afterwards
> > protein is denatured
What protein is created from 2 identical subunits which is more efficient to create? A Haemoglobin B Albumin C Collagen D HIV protease dimer E Myosin
OPTION D
dimer - clues in the name
> efficient and less chance of an error
as its assmeble at the quaternary levle
Which amino acid is a helix breaker? A Lysine B Histidine C Cysteine D Proline E Tyrosine
OPTION D
proline cannot rotate as side chain is bonded back to amino gorup
> tyrosine is detabliser as it has a big bulky side group
What are some key features of the protein structure of collagen?
Every 3rd a.a. = glycine
High proportion of proline (less flexibility, enforces KINKS in chain)
High proportion of hydroxyproline (proline modified after incorporation into protein)
in competitive inhibition what happens A V-max increases, Km constant B V-max constant, Km increases C V-max constant, Km decreases D V-max decreases, Km constant
OPTION B
v max the same but km increaes as you need more substrate to overcome inhibitor
> km/ km apparant for enzyme-inhibitor
> > enzymes are still functional so have the same vmax
in irreversible inhibition
what happens to Vmax + Km?
different vmax as there are LESS fucntional enymes
> functional enzymes work witht eh same affinitiy thoug
name some hydrophobic and hydrophilic aa (side chains)
Val, Leu, Phe - hydrophobic
Asp, Lys, Ser - hydrophilic
> they stay together in their groups during the ‘‘hydrophobic effect’’
decribe ‘‘hydrophobic effect’’ what occurs? when thinking about teritary structure (protein folding)
- hydrophobic collapse as water surrounds the hydrophobic molecules making them immobile = less entropy
- if water becomes free then energy becomes available for protien to fold
If the specificity constant of an enzyme is high…
It is a ‘good’ enzyme
kcat is high
km is high
It is a ‘good’ enzyme
kcat is high
km is low
It is a ‘good’ enzyme
kcat is low
km is high
OPTION B
hihg turnover rate and uses not a lot of substrate to do it
a plot of substrate concentration against reaction velocity generates what type of curve? A horizontal line B sigmoid C hyperbolic / curved D directly proportional E inversely proportional
OPTION C - is a nice curved line that plateaus
for competitive inhibition, which statement is incorrect?
A irreversible
B an inhibitor with the same shape as the substrate blocks the active site
C Vmax stays the same
D Km increased
E the amount of substrate available will be increased
OPTION A
competitve is reversible
substrate accumualtes so Km also increases
Which of the following sidechains is hydrophobic? A Aspartate B Valine C Lysine D Serine
OPTION B
Valine has two methyl groups and a H group attached, these are non-polar hence the sidechain is hydrophobic
the central carbon in an amino acid is called what? alpha beta omega gamma delta
ALPHA CARBON
