Protein structure P2 Flashcards
what side is the N and C terminus on?
N-terminus on the left side and C-terminus on the right
what is a polypeptide?
long chain of AA
what is a protein?
large polypeptide with a biological function
what is considered a dipeptide?
two AA joined by one peptide form
which amino and carboxylate groups retain their charge in a polypeptide?
the terminus groups
are peptide bonds covalent or non-covalent?
covalent
what is the primary protein structure?
sequence of AA residues
what is the secondary protein structure?
local folding of the polypeptide backbone
-alpha helix and B-sheets
-long chain of AA
what is protein tertiary structure?
the 3D structure of a long polypeptide including all of its side chains
what is quaternary protein structure?
multiple subunits of polypeptide structures
what is the characteristic of polypeptide backbone rotation?
rotation of the backbone is limited
how many AA are there per turn of an alpha helix?
3.6
how many residues per H-bond are there in alpha helices?
the carbonyl O2 of each reisdue forms an H-bond with the backbone -NH grouo FOUR residues downstream
which AA in primary structure are close in secondary structure?
amino acids 3-4 residues apart in the primary structure are close in the secondary structure
why is proline not common in the middle of an alpha helix?
there is no hydrogen bound to the N
-CH2 is too large to fit and cyclic structure creates kinks in the helix
what 2 conformations are seen with B-sheets?
parallel and antiparallel sheets
which carbonyl and nitrogens form interactions with each other in B-sheets?
every NH and Carbonyl are forming interactions with each other
what types of structures are available to connect B-sheets?
irregular structures
-classified as secondary structures
what is the difference in H-bond stabilization between alpha helices and B-sheets?
in alpha-helices H-bonds are between the backbone CO and NH groups in the SAME helices
B-sheet H-bonds are between the backbone CO and NH groups of neighboring strands
what makes irregular secondary structures irregular?
they dont have repeating geometry
-alpha helices and B-sheets are regular due to each AA having the same conformation in the backbone
what groups can tertiary structures be classified into?
fibrous (elongated)
- insoluble in (aq), long protein filaments
-structural or connective proteins (collagen)
globular (compact)
-soluble in (aq)
-fold on themselves into compact structures with non-polar core and polar surfaces
what structures are expected to be seen on the exterior of the tertiary structure as compared to the core?
polar exterior: polar AA, irregular structures (interact with H2O to satisfy H-bond potential)
hydrophobic core: hydrophobic AA, regular structures
*AA 1-2 polar, AA 3-4 hydrophobic
what is the driving force that soluble globular proteins adapt their tertiary structure?
hydrophobic effect
what force is repsonsible for “fine tuning” and stabilizing secondary and tertiary structures?
weaker forces–> H-bonds and salt bridges
True or False: AA residues are capable of forming H-bonds with residues located in the same alpha helix AND neighboring helices
TRUE if they are polar
-serine
what are salt bridges?
electrostatic intersactions between closely positioned formal charged groups
form between (-) and (+) charges
what are disulfide bonds?
covalent bonds between closely positioned cysteine groups
- these are not formed with methionine because a thiol group (SH) is needed to be oxidized
-helps maintain structure; not a determinant
what is a domain in regards to protein structure?
a polypeptide segment that has folded into a single structural unit with a hydrophobic core
-proteins may contain multiple domains
what is a motif in regards to protein structure?
a short region of polypeptide with a recognizable 3D shape
- ex. zinc fingers
what are prosthetic groups?
non-peptide components that are permanently incorporated into a protein
-provide structure and functional chemical groups
what are 2 examples of prosthetic groups?
Zn 2+ in zinc fingers and Heme in hemoglobin
what is an apoprotein?
a polypeptide without its prosthetic group
what is a holoprotein?
a polypeptide with its prosthetic group
why are globular proteins easily denatured?
they are stabilized by weak non-covalent forces
-H-bonds/hydrophobic
-salt bridges
what factors have an effect on denaturation?
heat, pH, salt and detergents
what can break disulphide bonds?
reducing agents
how are quaternary structures named?
by number and type of subunits
-dimer, trimer, tetramer, pentamer
what are 2 identical quaternary subunits called?
homodimer
what are 2 non-identical quaternary subunits called?
heterodimer
what forces stabilize quaternary structures?
the same as tertiary
-hydrophobic interactions
-H-bonds, ion pairs (fine tuning)
true or false: polar amino acids in the hydrophobic core of a globular protein are involved in either H-bonding or ion pairs (salt bridges)
TRUE
-depending on protonation state
