Chapter 2 - Protein Composition and Structure - part 2 Flashcards
Polypeptide chains can change direction by making
reverse turns and loops.
Unlike alpha helices and beta strands, loops do not have
regular, periodic structures.
Alpha-Keratin is a member of a superfamily of proteins referred to as
coiled-coil proteins.
In coiled-coil proteins, two or more alpha helices can entwine to form a
very stable structure, which can have a length of 1000 Angstrom or more.
The two helices in alpha-keratin associate with each other by
weak interactions such as van der Waals forces and ionic interactions.
The most abundant protein in mammals is
collagen.
Hydroxyproline is
a derivative of proline that has a hydroxyl group in place of one of the hydrogen atoms on the pyrrolidine ring.
What is myoglobin’s role in the body?
Acts as the oxygen storage protein in muscle.
In an aqueous environment, protein folding is driven by
The strong tendency of hydrophobic residues to be excluded from water.
The polypeptide chain folds so that its ________ side chains are buried and its _______ side chains are on the surface.
hydrophobic; polar
Amphiphatic
Having both hydrophobic and hydrophilic parts.
Motifs
Small regions of protein three-dimensional structure or amino acid sequence shared among different proteins.
Domains
Polypeptide chains that fold into two or more compact regions that may be connected by a flexible segment of polypeptide chain, rather like pearls on a string.
Domains range from _________ amino acid residues.
30-400
Primary structure
The amino acid sequence.
Secondary structure
The spatial arrangement of amino acid residues that are nearby in sequence.
Tertiary structure
The spatial arrangement of amino acids residues that are far apart in the sequence and to the pattern of disulfide bonds.
Subunit
Each polypeptide chain in a protein containing more than one polypeptide chain.
Quaternary structure
The spatial arrangement of subunits and the nature of their interactions.
The simplest sort of quaternary structure is the
dimer.
Dimers consist of
two identical subunits.
The amino acid sequence of a protein determines its
three-dimensional structure.
Difference between cystine and cysteine
Cysteine is an amino acid, and cystine forms when two amino acids join together via a disulfide bond.
A protein is said to be denatured when
the protein is converted into a randomly coiled peptide without its normal activity.
The information needed to specify the catalytically active structure of ribonuclease is contained in its
amino acid sequence.
Conditions that lead to the disruption of any part of a protein structure are likely to
unravel the protein completely.
Proteins fold by progressive stabilization of intermediates rather than by
random search.
Small proteins can fold is less than
one second.
Levinthal’s paradox
The enormous difference in time between calculated and actual folding times in proteins.
The essence of protein folding is to retain
partly correct intermediates.
The free energy difference between the folded and unfolded states of a typical 100-residue protein is
42 kJ/mol
Nucleation-condensation model
Unstable transition states must exist between the denatured and native state in proteins.
The local sequence appears to determine only between __________% of the secondary structure of proteins.
60-70
ab initio prediction attempts to
predict the folding of an amino acid sequence without prior knowledge about similar sequences in known protein structures.
In knowledge based prediction methods,
an amino acid sequence of unknown structure is examined for compatibility with known protein structures or fragments therefrom.
Intrinsically unstructured proteins (IUPs)
Proteins that, completely or in part, do not have a discrete three-dimensional structure under physiological conditions.
Unstructured regions are rich in
charged and polar amino acids with few hydrophobic residues.
IUPs appear to be especially important in
signaling and regulatory pathways.
Metamorphic proteins
Proteins that appear to exist in an ensemble of structures of approximately equal energy that are in equilibrium.
Chemokines are
small signaling proteins in the immune system that bind to receptor proteins on the surface of immune-system cells, instigating an immunological response.
Amyloidosis
a rare disease that occurs when an abnormal protein, called amyloid, builds up in your organs and interferes with their normal function.
Acetyl groups attached to the amino termini of many proteins makes the proteins
more resistant to degradation.
The addition of a fatty acid to an alpha amino group or a cysteine sulfhydryl group produces
a more hydrophobic protein.
The addition of sugars makes proteins more
hydrophilic.
