B1 protein structure and function Flashcards
amino acids are chiral, what does this mean
4 different groups are bonded to a tetrahedral a-carbon
what are the two mirror image forms of amino acid
what is the only isomer found in proteins
L and D isomer
only L isomer exist in proteins
what do free amino acids in a sol at neutral H exist as
dipolar ion
in dipolar ion aa what are the groups that are charged
amino group (NH3+)
carboxyl group (COO)
what 3 ionisation states exist and how do they vary
protonated
zwitterionic form
deprotonated
the 20 aa found in proteins have unique side chains that vary in what
size
shape
charge
hydrogen bonding capacity
hydrophobic character
chemical reactivity
what aa have nonpolar R groups
proline
leucine
methionine
isoleucine
glycine
alanine
valine
-phenylalanine
-tryptophan
what aa have polar R groups
serine
threonine
cysteine
asparagine
glutamine
-tyrosine
-histadine
-lysine
-arginine
-aspartate
-glutamate
what aa have aromatic R groups that are nonpolar
phenylalanine
tryptophan
what aa have aromatic R groups that are polar
histidine
tryosine
what aa have +ve charged R groups
aromatic R groups
polar R groups
histidine
what aa have -ve charged R groups that are polar
aspartate
glutamate
peptide bond formation is carried out by what reaction
condensation
releases water
primary protein structure
aa sequence
what can be said about the polypeptide chain in terms of its formation
has directionality
amino terminal end is taken as the beginning of the pp chain
what is the backbone and variable part of the polypeptide
backbone- repeating part
variable part- distinctive aa side chain
what bonding potential does the backbone have and why
hydrogen bonding
carbonyl groups and H atoms that are bonded to the nitrogen of the amine group
how many aa do most proteins consist of
50-2000
what is protein mass referred to as
daltons
1 dalton= 1g mol -1
in some proteins what can the pp chain be cross linked by and how
disulphide bonds
form by the oxidation of two cysteines
what are the cross linked cysteines called
cystine
what can be said about the peptide bonds shape
planar
6 atoms (Cα,C, O, N, H, Cα) lie in a plane
the peptide bond has partial double bond character, why and what does this result in
resonance
thus rotation about the bond is prohibited
what form of peptide bond is strongly favoured and why
trans form
because of steric clashes that arise in the cis form
where in the amino acid chain is rotation permitted
about the N-Cα bone
(the phi Φ bond)
about the Cα- carbonyl bond
(the psi ψ bond)
rotation in the aa chain allows proteins to do what
to fold in many different ways
what 2 things make protein folding possible
restrictions by the rigidity of the peptide bond
restricted set of allowed Φ and ψ angles (steric hindrance)
what is the secondary structure
the 3D structure formed by hydrogen bonds between peptide NH and CO groups of aa that are near each other in primary structure
what are 3 examples of secondary structure
alpha a-helix
beta b-strand
turns
appearance of a-helix
tightly coiled rod like structure
R groups sticking from axis of the helix
what parts of the a helix backbone do not form hydrogen bonds
those at the end of the helix
what is the a helix stabilised by
intrachain hydrogen bonds
are a helices left or right handed
right
what are b-sheets formed by
adjacent b-strands
what can be said about b-strands in contrast to a-helix
b-strand is fully extended
what are b sheets stabilised by
hydrogen bonds between the polypeptide strands
what positions could b-sheets be in
parallel
antiparallel
mixed
and may be flat or twisted
polypeptide chains can change directions with b-turns
what are they
hairpin turns- reverse turns
omega loops
bigger, irregular
what does the tertiary structure refer to
the spatial arrangement of aa that are far apart in the primary structure and it refers to the pattern of disulfide bond formation
size and space of globular proteins
very compact
little/no empty space in interior of globular proteins
what does the interior of globular proteins consist of
mainly hydrophobic aa
what does the exterior of globular proteins consist of
charged and polar aa
what is to be said about the distribution of hydrophobic/philic aa in membrane proteins
reverse distribution
hydrophobic exterior
water filled hydrophilic channel
(porin (PDB 1PRN))
what are motifs
supersecondary structures
combinations of secondary structure
what are domains
an independent folding unit of the 3D protein structure
what is the role of b-mercaptoethanol in regards to disulphide bonds
reducing
reduced disulphides and is itself oxidised forming dimers
what is the quaternary structure
proteins composed of multiple polypeptide chains (subunits)
what does the aa sequence determines
the folding of a protein into its 3D structure
what occurs after translation which determines many proteins fate in the cell
post translational modifications
examples of post translational modifications
-converting a proprotein by proteolytic cleavage to a mature protein
-addition of various chemical groups
-small proteins like ubiquitin
-fatty acids like myristoyl or prenyl groups
-branched glycosylations
-glycosyl phosphatidyl inositol (GPI) anchors
what 3 groups can undergo post translational modification by the addition of a chem group
-N terminal amino group
-C terminal carboxyl group
-side chains of amino acids throughout the length of the protein
lack of appropriate protein modification can result in
pathological conditions
alack of hydroxylation of proline in collagen results in
scurvy (vit C deficiency)
lack of carboxylation of clotting proteins results in
haemorrhaging (vit K deficiency)
