Ch.2: Protein Structure and Function I Flashcards
structure=
function
what are some functions of proteins
Transport, Regulation, Structure, Signaling, and Movement
What part of the amino acid determines how the protein is able to fold?
describe primary, secondary, tertiary, and quaternary structures
The R group determines folding.
Primary: principal determinant of overall protein conformation- sequence
Seocondary: more stable arrangements such as alpha and beta - local folding- held together by hydrogen bonds
tertiary: long range folding and more stable 3d structures
quaternary: proteins interact with themselves or other proteins forming the quaternary structure - multimeric
why is the primary sequence important?
the primary aa sequence is the ultimate determinant of final protein structure (and thus function)
which way do proteins go.
in the linear formation of peptide bonds, which is the nonvairant and which is the variable regions? Which is linear, which sticks out?
from amino terminus to carboxyl terminus
- the R groups stick out and these are the variable regions while the
- peptide backbone is nonvariant: consists of amide, alpha carbon, carbonyl C and the oxygen atoms
be able to draw the peptide bond formation btwn 2 amino acids
practice
the peptide bond contributes to protein structure and function through what 3 qualities?
1) peptide bonds are planar and do not allow rotation
2) therefore restrict 3D conformation of proteins
3) because they are planar, they make the R group stick out and they are able to contribute to folding with covalent and non covalent bonding
which carbons in amino acid chain rotate?
the alpha carbons connected to the R group, but the R group may sterically inhibit rotation
why are the R groups important in folding
they contribute to the folding as well as protein function.
- they can also form interactions with other biomolecules in cell membranes
describe an alpha helix? How often are the turns?
where are the bonds formed?
what disrupts formation?
where are the R groups
formed when polypeptide chain twists around on itself in a cylinder
- hydrogen bonds are formed between the BACKBONE- not the R groups as you would think.
- R groups stick out from the central plane
- hydrogen bond occurs between H attached to the Nitrogen and the oxygen of the carbonyl in the next turn.
- bc peptide bonds are planar, there are restrictions in frequency of turns. 4 aa per turn, but really 3.6 bc of interaction btwn a terminus and C terminus so a little shorter turns
- proline is a ring shape making it very rigid so it disrupts formation
describe the beta sheet
what are the 2 types?
comprised of adjacent strands or within the same protein
- parallel: A-C terminus is the same for each strand
- antiparallel: A-C terminus is opposite
- R groups stick out both above and below the plane of the sheet
- H bonds btwn backbone atoms of the strands
describe a beta turn
where are they typically found? (location)
what causes this?
- 4 aa that form a sharp bend and reverse the direction of the polypeptide background
- usually found on the surface of the protein
- caused by proline and glycine : proline has ring and glycine has no side chain therefore give sharp turn
characteristics of the __ determine tertiary structure by ___ interactions
-what are these interactions?
which aa tend to be on the outside/inside
R group determines folding by non covalent interactions (except sulfur is covalent and very strong for tertiary)
- hydrogen bonds, ionic interactions, van der waals forces, and hydrophobic interactions
- polar and charged aa tend to be on the outside and hydrophobic on the inside
what are protein motifs/domains?
how is this?
similar secondary and/or tertiary structures that can be formed from different aa primary sequence but still have similar structure
usually because the qualities of the aa are the same such as replacing a polar aa for another polar aa
describe the 3 protein motifs discussed in class. what is the turning important for?
1) coiled- coil motif:
two proteins with hydrophobic aa on the inside will coil around each other. this also allows proteins to dimerize
-can also have leucine zipper where you see a leucine every 2nd turn or every 7 aa and they are important for transcription factors to bind
- turning is important for stability
2) helix-loop-helix motif where loop region can sometimes bind metals ions like calcium
3) zinc-finger motif (also important for transcription factors)
- cluster of (2) HISTINE and (2) CYSTEINE that bind to zinc.
- sticks out like a finger
* also important for DNA binding. the finger regions make non covalent interactions with base pairs in the major grooves of the DNA helix
