Lecture 9: The Structure of Proteins Flashcards
the sequence of amino acids is specified by the __ sequence encoding the protein
gene
amino acid polymers of less than 50 amino acids are called __
peptide
a peptide bond is formed between which two groups in a peptide chain?
carboxyl group of the first and the amino group of the second
the H and R groups are opposite the ___ in a peptide bond to avoid steric clash
o in the carbonyl
the equilibrium of making a peptide bond favours the ___ side
left (hydrolysis)
why does the peptide equilibrium favour the hydrolysis rather than synthesis?
because the synthesis requires free energy
the alpha carbon can always be identified because it has the ___ attached to it
R group
each amino acid in a peptide chain is called a __
residue
every peptide chain begins with a ___ residue and ends in a __ residue
amino, carboxyl
the amino acid at the beginning of the chain is called the __
amino / N terminus
the amino acid at the end of the chain is called the __-
carboxly / C terminus
the geometry of an aa about a peptide bond is __
planar
what makes the peptide bond rigid? (not free to rotate)
resonance from the carboxyl makes the bond not purely single and therefore unable to freely rotate
the psi and phi bonds flank the ___ of each amino acid
alpha carbon
what bonds are free to rotate in amino acids?
the phi and psi bonds
the phi bond forms between the alpha carbon and the
amino group
the psi bond forms between the alpha carbon and the
carbonyl group
what does a Ramachandron plot show?
the permissible phi and psi bond angles allowed in a polypeptide backbone
the range of permissible angle combinations reflect the ___ and ___structure of proteins
secondary and tertiary
the polypeptide structure will have inherent __ and ___ within the constraints dictated by the permissible angles
flexibility and mobility
the secondary structure of proteins is stabilized by __ bonds between N and carboxyl groups in linear squence
H bonds
due to combination of bond angles and H bonding effects, certain aa segments ____ form secondary structures
spontaneously
what are the 3 types of secondary structures?
aplha helix , beta sheets, turns and loops
proteins can be made exclusively of alpha helix/beta sheets, or a mix of both (T/F)
true
turns and loops function to __
connect helices or sheets together
alpha helixes are segments of amino acids that form ___ handed helical structure (rotates ___ (cw.ccw)
right; clockwise
what is the average length of an alpha helix?
10 amino acids
there are about ___ amino acids per complete turn along the the alpha helix
3.6
in the alpha helix, every ___ amino acid interacts via hydrogen bonding
4
side chains extend in what direction with respect to the helix?
outwards
what makes some amino acids unsuited for helix formation?
geometry or size of side chains
about ___ % of all soluble proteins are composed of alpha helices
25
the B sheets are made by multiple __ of amino acids in a ___ sequence rather than coiled in a helix
adjacent segments; fully extended
adjacent segments in a B sheet interact by __ interactions
hydrogen bonding
adjacent B strands can be in anti-parallel or parallel (T/F)
true
in antiparallel B sheets, each amino acid is bonded to __ on the other strand
one amino acid
in parallel B sheets, each amino acid is bonded to __ on the other strand
2 different amino acids
in parallel B sheets, the two strands run in the ___ direction
same
in antiparallel b sheets, the two strands run in the ___ direction
opposite
B strands associate to become __
B sheets
B sheets are stabilized by intracellular ___ bonds
H
arrows representing B sheets point in the direction of the ___ terminal end
carboxyl
Beta sheets can be flat, but most adopt a ___ shape
twisted
what two amino acids participate in forming turns?
proline and glycine
there is open space in the interior of a protein (T/F)
no; little to none
name 5 things that stabilize tertiary structure
- charge interactions
- H bonding
- van der waal between side chains
- hydrophobic effect
- disulphide bonds b tween cysteine side chains
myoglobin is an example of a __ protein
globular
myoglobin is an extremely compact molecule made of __ polypeptide chain(s) of ___ (#) amino acids
1; 153
about 70% of the myoglobin structure is made of __
alpha helices
tertiary structures of many proteins can be divided into __ and ___ units
structural and functional
some proteins fold into multiple tertiary structures called __
domains
each domain may posses a unique ___ that may be quite functional even id separated from the protein
enzymatic function
discrete sub-structures in a protein with special structural/functional significance are called __
motifs
what motif is typically found in proteins that bind double-stranded DNA?
helix–turn–helix
each polypeptide chain in a protein complex is called a __
subunit
quaternary structure refers to the arrangement of ___ and the nature of their interactions
subunits
what is homotypic association?
proteins assemble within each other
what is heterotypic association?
different proteins assemble into multi-subunit complexes
example of a heterotypic protein
DNA polymerase
