Lecture 1 Flashcards
what are the general functions of proteins?
Enzymes, plasma membrane proteins, signaling, structural proteins, motor proteins, anitbodies, hormones
who coined the term protein?
Jons J Berzelius
which amino acids have sulfur groups?
cysteine and methionine
which amino acids have -OH groups?
tyrosine, serine, threonine
how are peptide bonds formed?
a-carboxyl group joined to a-amino group
includes a loss of water molecule
what kind of bond is a peptide bond?
planar bond
how many bonds do amino acids contribute to protein backbone?
3
steric (spatial) effect
effect in which the shape of a molecule influences its reactions
why are peptide bonds rigid?
carbonyl carbon atom and nitrogen atom has partial double-bond character
which end of a polypeptide chain is the beginning?
(amino end or carboxyl end)
amino end (N terminal)
polypeptide backbone
repeating atoms along the core of the polypeptide chain
what bonds constrain protein folding? what type of bonds are they?
weak non covalent bonds
hydrogen bonds, ionic bonds, van der waals
hydrophobic interactions
minimize disruption of hydrogen bonding between water molecules
where are non-polar side chains of amino acids? (in terms of hydrophobic interactions)
cluster in the interior of proteins
where are polar side chains of amino acids? (in terms of hydrophobic interactions)
outside of the proteins
hydrogen bonded to other polar amino acids or to polypeptide backbone
disulfide bonds
covalent links between the sulfur atoms in the side chains of cysteins
what is the function of disulfide bonds?
stabilize protein structure (folding or mediate attachment of protein subunits)
intrachain disulfide bonds
joining two parts of the same polypeptide
interchain disulfide bonds
joining two different polypeptide chains
where do disulfide bonds form?
ER
why can’t disulfide bonds be formed in the cytosol?
high concentration of reducing agents in the cytosol
what are the four levels of protein structure?
primary, secondary, tertiary and quaternary
primary protein structure
order/sequence of covalently linked amino acids
tertiary protein structure
3D organization of polypeptide chain
- steric relationship of amino acids that are far apart in linear sequence
secondary protein structure
folding of polypeptide chains (maintained by repetitive hydrogen bonding)
- steric (spatial) relationship of amino acids that are close to one another in the linear sequence
-a-helix and b-pleated sheets
quaternary protein structure
complete 3D structure of multi-subunit protein complexes (the way protein chains are packed together)
who sequenced the first protein? what kind of protein?
Frederick Sanger; bovine insulin
how are a-helix and b-pleated sheets bonded?
hydrogen bonding of amino and carbonyl groups in polypeptide backbone
no bonding between side chains of amino acids
what determines the conformation of a protein?
amino acid sequence
how many possible primary protein sequences can exist?
20^n
how many protein sequences are known?
500,000
where does the H-bond occur in a-helix?
every fourth peptide (3.6 amino acids)
coiled- coil
a-helices when they wrap around each other (triple helix)
how do colied-coils form?
two or three a-helices have their nonpolar side chains on one side -> wraps around each other with side chains facing inward
what proteins contain a-helices?
cell membrane proteins (transport proteins and receptor)
-nonpolar side chains
-rich in areas that cross lipid bilayer
what factors destabilize a-helices?
- electrostatic repulsion between similarly charged R groups
- steric hinderance due to bulky substitutions on the B- carbons of R group
what amino acid is incompatible with the a-helix?
proline
what protein was b-pleated sheets first identified in?
fibroin (silk)
why is a amino acid incompatible with the a-helix?
proline b/c it causes bends in the polypeptide backbone
- proline amino group cannot participate in H bonding
- rotation around the bond between nitrogen of proline is restricted
similarities of B-sheet and a-helix
both involve H bonding between carbonyl and amino groups of peptide bonds
differences of B-sheet and a-helix
- H bonds form between different parts of single chain (intrachain vs interchain)
- bonds are perpendicular on b-sheet vs parallel in a-helix
parallel pleated sheet
h bonded peptide chains run in same direction
antiparallel pleated sheet
H bonded peptide chain run in opposite directions
reverse turns
regions of secondary structure where the chains change direction or fold back
supersecondary structure
secondary structures that combine (BaB, aa, B-meander unit, greek key)
motifs
repeated combinations of supersecondary structure within a protein (usually short repetitive units)
domain (module)
- specific region of protein that can fold independently of the rest of the protein into a discrete stable structure that has its own function
- modular units that construct larger proteins
- smaller proteins = single domain
- larger proteins = several dozen domains connected by unstructured polypeptide chains
domain shuffling (multidomain proteins)
DNA sequences encoding each domain accidentally joined, creating new gene
how many domains does fibronectin have?
four of fibronectin type 3 domains
