L7. Protein structure & function I Flashcards
explain the structure of a protein
- polypeptide backbone
- R group (side chain)
- N-terminus
- C-terminus
protein structure - R group
- part of the amino acid that is not involved in forming peptide bonds
- gives each amino acid its unique properties
protein structure: R group - what unique properties may it have
- Hydrophobic
- Hydrophilic
- Can have a positive or negative charge
explain weak noncovalent bonds
- they allow proteins to bind to each other to produce larger structures in the cell
- 3 types:
1. van der Waals
2. ionic (electrostatic) attractions
3. hydrogen bonds
weak noncovalent bonds - van der Waals
- Really weak and has fluctuation in the charge of individual groups
- the individual groups will stick together bc of fluctuation in charges
weak noncovalent bonds - ionic (electrostatic) attractions
- Positive or negative charges that attract and facilitate an interaction
- in absence of water: strong
- in presence of water: interactions become shielded and become weak
- the bond is also weakened by ions
weak covalent bonds - hydrogen bonds
- Oxygen interacting with hydrogen
- Can interact across polypeptide chains, between different nucleotides, between interactions with water or solutions
explain hydrophobic interactions
- water forces hydrophobic groups together
- this can then result in a protein being folded with hydrophilic regions being outside and interacting with the water while hydrophobic regions are pushed inside the protein
define denaturation
- a protein being unfolded and losing its natural state
- can happen through treatment with solvents
denaturation - examples of solvents
- urea
- high concentrations can denature a protein
- removing the urea causes the protein to renature
define renaturation
a protein refolding into its original conformation
what are the levels of protein organization
- primary
- secondary
- tertiary
- quaternary
levels of protein organization - primary structure
- amino acid sequence
- can be resolved biochemically
levels of protein organization - secondary structure
- stabilized by hydrogen bonds
- alpha helixes and beta pleated sheets form within certain segments of the polypeptide chain
levels of organization: secondary structure - alpha helixes
- it is generated when a a single polypeptide chain turns around on itself
- depending on the twists, they can be either right or left handed
levels of organization: secondary structure - where are alpha-helixes typically found
they are often found embedded in cell membranes as transport proteins and receptors
levels of organization: secondary structure - coiled coil structure
- when two alpha helices wrap around one another to form a stable structure
- minimizes exposure to hydrophobic amino acid chains to aqueous environments
levels of organization: secondary structure - beta pleated sheet
- created when hydrogen bonds form between segments of a polypeptide chain that lie side by side
- can be parallel or antiparallel
levels of organization: secondary structure - parallel beta sheet
neighboring segments run in the same orientation
levels of organization: secondary structure - antiparallel beta sheet
neighboring segments run in the
opposite orientation
levels of organization: secondary structure - amyloid fibers
- they are created when beta sheets are stacked together
- these are insoluble protein aggregates
- causes neurodegenerative diseases and biofilms
levels of organization: secondary structures - how can a protein turn into amyloid fibers
- a normal protein can adopt an abnormal, misfolded prion form
- another normal form and a prion form may bind and the normal one can turn into a prion
- abnormal prion proteins will propagate and aggregate to form amyloid fibers
explain how prions are infectious
- they are an infectious protein
- they are able to withstand high temperatures, making it hard to denature
- causes numerous diseases including: MAD cow disease
chaperon proteins - isolation chamber
- a partially folded polypeptide chain is put in the chamber and the cap it put on top
- the polypeptide chain will be folded correctly inside and released when the cap dissociates
explain chaperon proteins
- these proteins assist with protein folding
- they bind to partly folded chains and help fold
chaperon proteins: isolation chambers - why is this needed
so a single polypeptide can fold without the risk of forming aggregates in the crowded cytoplasm
what are heat shock proteins
- they are chaperons that respond to elevated body heat
- function is to re-fold miss-folded proteins
levels of organization - tertiary structure
- the full 3D conformation formed by an entire polypeptide chain
- consists of alpha helices and beta sheets (can have one or a combination of both)
levels of organization: tertiary structure - what forces hold it
- hydrophobic forces
- hydrogen bonds
- disulfide bonds
levels of organization - quaternary structure
- a complex made of more than one polypeptide chain
- subunits are connected via noncovalent bonds and disulfide bonds
- Can form a long chain or dimer to create a functional unit
levels of organization: quaternary structure - examples
- hemoglobin: 2 alpha helices and 2 beta sheets
- tubulin
- actin filament
- collagen
- elastin
levels of organization: quaternary structure - what are disulfide bonds
- S-S bonds
- covalent linkages between the thiol groups of two cysteine residues
- reinforces the protein’s most favored conformation
- can happen through physical interaction
levels of organization: quaternary structure - how can you utilize disulfide bonds in a lab setting
- Can add reducing agent to break bonds for studying proteins
- Can done in-vito or in-vivo
