Protein Localization & Structure Flashcards
What are the Primary, Secondary, Tertiary, and Quaternary Structures of Proteins?
Primary Structure refers to the linear amino acid sequence
Secondary Structure refers to the folding of the peptide chain into domains and motifs (α helix, β sheet, and random (coil) structures)
Tertiary Structure refers to the full 3D confirmation of an entire polypeptide chain
Quaternary Structure refers to the protein complex of more than one polypeptide
What are the different types of secondary structures of a protein?
Alpha Helices and Beta Pleated Sheets
What are the types of interactions in a protein folding and assembly?
Noncovalent bond
Covalent bonds
Disulfide bonds
This refers to the forces responsible for pushing non-polar amino acid chains into the center and is supported by van der Waals interactions to maintain compactness. Also includes h-bonds and electrostatic interactions.
Noncovalent bonds
Stabilizes extracellular proteins through covalent bonds
Covalent cross-linkages
Covalent cross-linkers that form through oxidation and are removed by reduction
Disulfide bonds
Protein can express the cells but can be localized differently (i.e. in cytosol or ER lumen) separating based on organelle type, what determines this?
Signal sequences (peptide)
What is the difference between protein motifs and domains?
Motifs: are peptides found in several proteins but does not necessarily relate to function
Domains: self-contained section of a protein that is capable of independently folding into its three-dimensional structure.
What methods are used to determine Primary, Secondary, Tertiary, and Quaternary Structures of Proteins?
Primary Structure:
Edman Degradation: Sequentially removes and identifies amino acids from the N-terminus of a protein.
Secondary and Tertiary Structure:
1. X-ray Crystallography: Provides detailed information about the arrangement of atoms in a crystal lattice, which can be used to infer secondary and tertiary structure.
2. Nuclear Magnetic Resonance (NMR) Spectroscopy: Analyzes interactions between atomic nuclei to infer local structural features, including secondary and tertiary structure.
Quaternary Structure:
1. X-ray Crystallography: Can reveal how individual protein subunits are arranged within a larger complex.
2. Native Gel Electrophoresis: Separates proteins based on their size and charge under native conditions, providing information about their quaternary structure.
What is the purpose of using trypsin in LC-MS/MS protein structure determination?
Proteolytic digestion. Its purpose is to cleave proteins into smaller peptides, facilitating their analysis by mass spectrometry
Idk why I made this into an entire separate section but the pdf is just really short
Idk, drink water?
LC-MS/MS stands for? What is it used for?
Liquid Chromatography-Mass Spectrometry, used for unknown protein detection/sequencing of unknown peptides
