1.7 Protein structure and self-assembly Flashcards
polypeptide
long chain of amino acids
protein
filed chains of amino acids
peptide
short chain of <50 amino acids
amino acyl residues (don’t need to know but good to be familiar to avoid confusion
in a peptide = amino acids with either OH (from Carboxyl group) or H (from the amino group) removed in the process of peptide bond formation
equivalents of one H2O removed per peptide bond
directionality of proteins
always in the N -> C direction (amino -> carboxyl end)
amino acyl residues are number 1 to “n” in this direction
what is the backbone of the polypeptide chain
everything BUT the R group
hydrophobic Amino acids
have NON-POLAR side chains
Hydrophilic Amino Acids
CHARGED and POLAR side chains
acidic amino acids
NEGATIVELY charged
basic amino acids
POSITIVELY charged
important of sequence and structure in proteins
sequence determines structure
structure determines function
Primary structure
sequence of amino acids in a protein
the makeup of R-groups in a polypeptide chain determines the structure of a protein since the backbone is the same and AA are differentiated only by the different groups!
sequence determines the protein’s 3D structure
secondary structure
results from interactions of nearby amino acids
alpha helices and beta sheets
both structures are stabilized by H-bonds as they form between the backbone of a folding polypeptide chain
backbone interactions (secondary structure
carbonyl group in one peptide bond and an amide group in another form repetitive H-bonds
beta sheet
it a flat wobbly thing
adjacent strands can run in the same direction (parallel) or in opposite directions (antiparallel)
antiparallel is more stable
tertiary structure
3D shape of a protein
what interactions are tertiary structures stabilized by
side-chain interactions
- non-covalent and disulphide bonds
annnnnd interactions between side chains and backbone atoms
quaternary structure
multiple folded polypeptide chains!
multiple subunits
form, interact, and are stabilized by non-covalent interactions
properly folded proteins will be…
energetically favourable for the whole system
denaturation
- protein unfolding
- due to disruption of non-covalent interactions
- can happen by changing pH, temperature, etc. (basically a change in surroundings)
- not all proteins can denature and then regain function
STRONG interactions between side chains = more difficult to denature
WEAK interactions between side chains = easy to denature
basically…
STRONG interaction = more STABLE protein
integral membrane proteins
aka transmembrane proteins
cross THROUGH the lipid bilayer
peripheral membrane proteins
are associated with the lipid bilayer on either side
NOT EMBEDDED in the lipid bilayer
why are easily broken bonds within folded polypeptide chains important?
more dynamic!!
stronger does NOT equal better
folded polypeptide chains have lots of non-covalent interactions
other factors that affect interactions
size of side chain
- can potentially increase the number of interactions
- small to big v.s. big to small (“fit”)
hydrophobic (ID-ID) interactions?
- lots of interactions make them very strong!
location in the protein
- interior vs exterior – charged and polar side chains tend to interact with water vs non polar side chains
how to approach substitution questions
- what is the interaction between the existing side chains? (R groups?)
- does the interaction increase, decrease, or No change if one A.A. is subsituted
- could this change the stability of the protein? what substitution results in the greatest change?
active site
protein folding brings specific amino acids close to each other to form the active site
conformation change
shape change
happened when substrates bind in the active site of enzymes
competitive inhibition
inhibitor binds to the active site of the enzyme, competing with the substrate and reducing the rate of the reaction
non-competitive inhibition
i.e. allosteric regulators
inhibitor binds to a site other than the active site, changing the shape of the enzyme and reducing the rate of the reaction
Amino acid residues
amino acids that are incorporated into a protein
what determines tertiary structure
determined by the spatial distribution of hydrophilic and hydrophobic R groups along the molecules
◊ As well!! As by different types of chemical bonds and interactions that form between various R grouops
○ Ionic
○ Hydrogen
○ Van der Waals
higher-order quaternary structure
many other proteins composed of two or more polypeptide chains or subunits with a tertiary structure that come together
* Polypeptide subunits may be either identical or different
○ Can influence each other in subtle ways and influence their function
