Protein Structure and Function Lecture 5 Flashcards
How can you distinguish between the L form and D form enantiomer?
The CORN rule; the amino acid reads CORN from left to right when the hydrogen is in the back
amino acids are asymmetric and have a chiral center (except ___), so they can exist as ____
glycine; enantiomers
If the pH is below the acid’s pKa, is the acid likely to be charged?
no it will be neutral; acids will either be neutral or have a -1 charge
what is the central dogma for protein sequencing from a DNA sequence?
DNA makes RNA makes protein
Interactions between side chains of aspartate and arginine at neutral pH would be ____.
ionic
most polypeptides contain between ___ and ___ amino acids
50; 2000
What is the average molecular weight for an amino acid?
110 daltons
the molecular weight of most proteins is between ____ and ____ daltons or ___ and ___ kD.
5500, 220,000; 5.5, 220
some proteins contain _____ bonds that cross link between the cysteine residues by the oxidation of cysteine.
disulfide
intracellular proteins often ___ disulfides while extracellular proteins often ____ them.
lack; have
____ proteins have a common ancestral protein.
homologous
phylogenetic trees based on ___ ____ are consistent with trees based on ribosomal ___ ____ or morphology.
protein homology; RNA sequences
cytochrome c is a very important protein in every cell; between many species, there are ___ conserved amino acids; eight are ____ and three are ___
22; glycine; proline
proteins with similar ____ normally have similar ____
function; structure
___ is more conserved than sequence.
structure
What is Levinthal’s paradox?
folding for most small proteins is extremely fast; the enormous difference between calculated and actual folding time
What protein did Christian Anfinsen work on to create Anfinsen’s dogma?
ribonuclease A
What is Anfinsen’s dogma?
For small, globular proteins, the native structure is determined only by the protein’s sequence. The native structure is a unique, stable, and kinetically accessible minimum of the free energy for a given environment.
Simplified: Primary structure determines tertiary structure.
Disulfide bonds form ___ the protein folds.
after
define denaturation
disruption of native conformation of a protein, with loss of biological activity (use heat or chemicals)
proteins fold ____ by ____ bonds and ____ interactions.
cooperatively; hydrogen; hydrophobic
what are the 4 principles of the protein folding problem?
- bury hydrophobic groups
- expose charged groups or neutralize with salt bridges
- expose polar groups or satisfy hydrogen bonding
- obey stereochemical restraints
___ ___ results in the disordered peptide condensing around a weakly ordered ___ ___, which is either a small turn or a short stretch of local secondary structure.
hydrophobic collapse; folding nucleus
hydrophobic amino acids are typically buried in the ___
core
The structures of ___ and ___ ___ are due to the hydrophobic effect.
micelles; soluble proteins
amino acids pack together like ___ ___ to fill the interior (or core) of a protein
puzzle pieces
___ represent the free energy potential of folding proteins
funnels
In protein folding, the __ ___ ___ assist subsequent ___ and ____.
first few interactions; alignment; folding
what is the driving force of protein folding? there is a large increase in ___ as ___ is released to bulk solvent
hydrophobic interactions (hydrophobic effect); entropy; water
Protein folding occurs by ___ ___. Partly correct folding ___ are retained because they are slightly more ___ than unfolded regions. Thus, proteins don’t fold ___ ___.
cumulative selection; intermediates; stable; completely randomly
what are the stages of protein folding?
- hydrophobic collapse
- nucleation-condensation
- partially structured intermediate
- native conformation
during the folding process, the polypeptide collapses into an intermediate ___ ___ due to the ___ effect. The backbone is then rearranged to achieve a stable ____ conformation.
molten globule; hydrophobic; native
____ collapse and ____ structure form at the same time
hydrophobic; secondary
What happens if the protein gets stuck while folding?
It’s either directed to a chaperonin to be fixed or protease to be degraded.
chaperonin assisted protein folding requires ___ through the ___ of several ___ molecules.
energy; hydrolysis; ATP
what do chaperonins do?
-prevent incorrect protein aggregation
for chaperonins, protein folding takes place inside the ___ ___
central cavity
two examples of chaperonin
HSP60; GroE
Who won the nobel prize in 1962 for “hemoglobin the 1st protein structure”?
max f. perutz
how do you bury the the hydrophobic side-chains in the core of a protein and still satisfy the strong dipole and hydrogen bonding needs of the peptide backbone?
the alpha helix (2ndary structure)
who discovered the alpha helix in 1951?
linus pauling
in an alpha helix, the ___ of residue 1 accepts a proton from the ___ or residue n+__.
carbonyl; amide; 4
in an alpha helix, how many residues are there per turn?
3.6
in an alpha helix, the H-bond is between atoms _ and __.
1; 13
for every turn of the alpha helix, there are between _ and _ H-bonds.
3;4
what is the pitch and rise of an alpha helix?
pitch: advance per helix turn; 0.54 nm
rise: advance per amino acid residue; 0.15 nm
___ ___ are often found on the surface of proteins.
amphipathic helices
what does amphipathic mean for an alpha helix?
one side of the surface of the alpha helix has hydrophilic AA’s and the opposite side has hydrophobic AA’s
residues are spaced ___ degrees apart in the helical wheel
100
with beta sheets, there’s no such thing as a ___ ___.
lone strand
____ beta sheets are more stable and stronger than ____ beta sheets due to the more ____ hydrogen bonds.
anti-parallel; parallel; linear
native conformation is achieved by rotating the main and side chain ___ ___.
torsion angles
what are the three torsion angles in the main chain?
omega; phi; psi
Between trans and cis isomers, there is a strong preference for ___ due to steric clash. ____ is a special case though. It permits both trans and cis conformers.
trans ; proline
