proteins Flashcards
homomeric proteins
heteromeric proteins
proteins that contain copies of the same polypeptides
proteins that are made up of different polypeptides
the alpha amino acid structure is common to all amino acids except?
Proline
features of an amino acid
the carboxyl group
amino group
hydrogen
a variant(side chain)
which side do we start from when naming amino acids?
the side closest to the alpha (chiral) carbon atom
what is the variant group of glycine?
a hydrogen atom
describe the structure of proline
the function of the cyclic structure in proline
the side chain is bonded to the alpha-amino nitrogen
it induces bends in the resulting polypeptide
oxidization of the SH group of a cysteine means?
the SH groups of two cysteines can be oxidized to form a dimer, which contains a covalent cross-link called
a hydrogen atom is lost from the group
a disulfide bond
features of amino acids with an acidic side chain
hydrophilic
negatively charged
polar
they have an extra carboxyl group
features of amino acids with basic side chains
hydrophilic
polar
positively charged
what is the function of histidine, and where is it found
helps to catalyze the making and breaking of bonds
it is often found in enzyme-active sites
what is meant by a physiological pH?
what is special about histidine when it is at physiological pH
refers to the pH that is typical and optimal for the normal functioning of living organisms
it can switch between being positively charged and neutral
state the features of cysteine that make it special
it is reactive, as it has the sulfhydryl group
Covalently links to other cysteine residues to form a disulfide bridge
state the features of Proline that make it special
it’s amino group is part of a ring structure
it lacks hydrogen bonds and therefore does not interact well in secondary structures
hydrophobic
produces kinks or hinges in proteins
the R group of glycine
is there a chiral carbon in glycine?
H
no, because, none of the carbons in glycine are bonded to four different atoms or molecules
what is the feature of a D-alpha amino acid
what is the feature of a L-alpha amino acid
it presents the NH2 group on the right side of the asymmetric-carbon
it presents the NH2 group on the left side of the asymmetric-carbon
of what optical configuration is the amino acids found in human proteins
the L-configuration ( they are L-alpha amino acids)
can amino acids absorb visible light?
what color are they consequently?
no, they cannot, and are therefore colorless
what is special about amino acids with aromatic side chains in regard to their spectral properties
at what wavelength do aromatic amino acids possess this special property
they have a characteristic UV absorption and therefore allow protein concentration to be spectroscopically estimated
280nm
how many aromatic amino acids are there?
name them
three
Phenylalanine
Tyrosine
Tryptophan
is proline an aromatic amino acid
no, because it does not have an aromatic ring structure
hydroxylation of amino acids
importance of hydroxylation
refers to adding hydroxyl groups to amino acids, typically to their side chains
they stabilize collagen fibres through hydrogen bonds(more H bonds)
increases the polarity of the amino acid
makes amino acid more hydrophillic
what can hinder the hydroxylation of amino acids in humans, and what effect would this have on the person
vitamin C deficiency
could cause scurvy
methylation of amino acids
refers to adding a methyl group onto an amino acid
importance of histone methylation
it regulates gene expression (genes closer together, so less expressed)
is which protein is N-methyllysine found
myosin
carboxylation of amino acids
adding a carboxyl(COO-) group to an amino acid
the effect of vitamin K deficiency
hinders the carboxylation of glutamate, causing clotting problems and hemorrhage
phosphorylation of amino acids
the addition of phosphate groups to amino acid residues
in eukaryotes, proteins may be phosphorylated at which amino acid residues
serine
tyrosine
threonine
zwitterions
A zwitterion (also known as an inner salt or dipolar ion) is a molecule or chemical species that contains both positive and negative electric charges within the same molecule, resulting in a net charge of zero
at physiological pH, amino acids exist as ……………….. ions
dipolar (zwitterions)
the ionization state of an amino acid varies with pH, true or false?
what is typically the net charge of amino acids at acidic pH?
true
+1
what is typically the net charge of amino acids at basic pH?
-1
amino acids are ……………. linked via peptide bonds
covalently
are peptide bonds ever charged?
no, the peptide bond is uncharged at any physiological pH of interest.
define these structures of proteins;
Primary
Secondary
Tertiary
Quaternary
the sequence of amino acids in polypeptide chain
Simple structures resulted from arrangements in space between adjacent amino acids
The complex 3D shape of the protein
this is when there is more than one polypeptide chain in a protein structure
knowledge of the primary structure of an amino acid can help predict
Final 3D structure of a polypeptide
Mechanism of action of a protein
Associated pathologies of a protein
forms of the secondary structure of a protein
alpha helix
beta pleated sheets
facts about the alpha helix form of polypeptides
It is a spiral structure, consisting of a tightly packed, coiled polypeptide backbone core.
The side chains of the component amino acids extend outward.
Stabilized by hydrogen bonds.
Each turn of an α-helix contains 3.6 amino acids.
bonds present in the tertiary structure of amino acids
disulfide bonds
hydrogen bonds
ionic bonds
London forces
hydrophobic bonds
examples of proteins with a quaternary structure
haemoglobin
collagen
factors that can cause proteins to denature(change in the shape of the active site of a protein)
can proteins ever be renatured (i.e is denaturation reversible)
extreme pH
extreme temperatures
extreme levels of specific chemicals like urea
yes, but this is rarely done
