Lecture 5 Flashcards
general formula of an amino acid
alpha carbon in center amino group carboxyl group (20) side chain hydrogen
at pH 7 the amino acid is a
zwitterion
all amino acids have a stereoisomer except
glycine
only – amino acids are found in proteins
L
stereoisomers have same – but different –
same physical characteristics but different biological characteristics
Basic side chains (+)
lysine, arginine, histidine
Acidic side chains (-)
aspartic acid, glutamic acid
Nonpolar side chains
alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan glycine, proline, cysteine
uncharged polar side chains
asparagine, glutamine, serine, threonine, tyrosine
a polypeptide is a polymer of –
amino acids
the primary structure of a protein is the –
specific linear sequence of AA
the – of AA makes each protein different
arrangement
AA are linked by –
covalent peptide bonds
backbone of a peptide chain has directionality
N-terminus –> C-terminus
What makes up the peptide backbone?
N of amino group, alpha carbon, C of carboxyl group
– determine the properties of the protein
side chains
a – in the primary sequence can cause devastating results in the structure and function of a protein
single change
secondary structure is determined by the –
peptide backbone interactions
the polypeptide backbone provides many sites for –
H-bond formation
Where can hydrogen bonds of the peptide backbone be found?
O of carboxyl and H of amino group
hydrogen bonds are between – residues in the backbone
nearly adjacent
How many residues per turn?
3.6
in an alpha helix, H bonds are – to the axis
almost perfectly parallel
alpha helices are abundant in –
transmembrane proteins
in B sheet the hydrogen bonds between backbone atoms in –
neighboring chains
the – contain extensive regions of B sheet
core of proteins
B-sheet produce – structures
rigid
H bonds are perpendicular to the backbone in – B sheet
anti-parallel
fixed bond angles in the backbone produce
a pleated contour
change the direction of a polypeptide
B turns
Most common residues in a turn
- glycine (small) can squeeze in small places
- proline bends the backbone
final folding of a single polypeptide
tertiary structure
proteins fold into a conformation with the
lowest energy state
Oil drop model of protein folding in a water environment
hydrophobic core and hydrophilic surface
a protein’s conformation (3D structure) is determined solely by
its linear sequence
protein domain
a substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable strucutre
a domain usually contains
40-350 residues
different domains of a polypeptides are usually associated with –
different functions
motifs is often a signature for a –
specific function
small structural domains
structural motifs
motifs are – structures composed of a defined arrangement of alpha helices and/or beta sheets
tertiary
structural motif
same structure but different sequence
sequence motif
same sequence and same structure
helix-loop-helix contains
2 alpha helices connected by a short loop
the loop is made up of
glutamate and aspartate
What would happen to the helix-loop-helix motif if the [Ca2+] decreases in the cytoplasm?
it will straighten out
coiled-coil structural motif
2 alpha helices wound around each other to form a rod-shaped protein
coiled-coil motif is composed of
repeats of 7 AA
coiled-coil is stabilized by the interaction of
the hydrophobic side chains of the 1st and 4th amino acids
protein domains are – from which larger proteins are built
modular units
at least 40% of human protein-coding gene can be assigned to – by sequence comparison
500 protein families
many large proteins have evolved through the joining of preexisting domains
domain shuffling
domain shuffling during vertebrate evolution has given rise to many – of protein domains
novel combinations
binding site
reacts with another molecule through non-covalent interaction
dimerization region
where two different polypeptides interact with one another
active site
region where catalysis takes place
regulatory site
binding site for molecule which may increase or decreases the activity of an enzyme through allosteric regulation
interactions between two or more protein subunits
quaternary structure
quaternary structure describes the – in multi metric proteins
number and relative positions of the subunits
2 identical protein subunits
homodimer
2 different protein subunits
heterodimer
protein subunit
one polypeptide chain
the most common covalent cross-linkage in proteins
disulfide bond
interchain disulfide bond
quaternary structure
intrachain disulfide bond
tertiary structure
the cysteine n side chain contains a – which can form a covalent disulfide bond to a second cysteine
reactive sulfhydryl group
disulfide bond usually exists
outside the cell (oxidizing environment)
protein molecules often serve as subunits for the assembly of large structures by –
non-covalent interactions
T/F: all structures held together by noncovalent bonds self-assemble
false
the special protein aggregate that cause prion diseases
amyloid fibril
normal functions fro – amyloid fibril
reversible
primary structure stabilized by
peptide bonds
secondary structure stabilized by
H bonds between groups along the peptide-bonded backbone
interaction between R-groups or between R-groups and the backbone stabilizes
tertiary structure
interactions beween R-groups, and between backbones of different polypeptides stabilizes
quaternary structure
steric limitation of – restrict the possible 3D conformations of atoms
planar peptide bonds
rotations around alpha carbon and N
phi
rotations around alpha carbon and C
psi
partially double bonded peptide created by –
resonance
folding of protein in vivo is promoted by
molecular chaperones
bind and stabilize newly synthesized or unfolded proteins thereby preventing these proteins to interact with other proteins and become degraded
molecular chaperone (Hsp 70)
form a small folding chamber into which an unfolded protein can be sequestered, giving it time and environment to fold properly
chpaeronin (hsp-60-like)
information directing a protein’s folding is encoded in its
amino acid sequence