Module 1 Flashcards
(26 cards)
What are the four levels of protein structure?
Primary: amino acid sequence
Secondary: alpha-helices and beta-sheets stabilized by hydrogen bonds
Tertiary: 3D folding due to side chain interactions
Quaternary: assembly of multiple polypeptide chains
Hydrophilic vs Hydrophobic Molecule
Hydrophilic: typically charge-polarized or capable of hydrogen bonding, making them soluble with water
Hydrophobic: not electrically polarized, unable to form hydrogen bonds, typically found in the hydrophobic protein core
Hydrophobic Amino Acids
Aromatic: phenylalanine, tyrosine, tryptophan (aromatic rings)
Aliphatic: alanine, valine, isoleucine, leucine, methionine (hydrocarbon chains)
Acronyms: Poor Tiny Terry, All Vasoline Is Leaking MAN
Hydrophilic Amino Acids
Basic: lysine, arginine (positively charged)
Acidic: aspartic acid, glutamic acid (negatively charged)
Polar, Uncharged: serine, threonine (OH), asparagine, glutamine (NH2) [hydrogen bonding]
What are the four special amino acids?
cysteine, glycine, proline, histidine
What makes Cysteine a special amino acid?
It forms disulfide bridges, stabilizing protein structure
What makes Glycine a special amino acid?
It is very small, the side chain is a single hydrogen, allowing tight turns in protein folding
What makes Proline a special amino acid?
Its cyclic structure forces a kink in the polypeptide chain
What makes Histidine a special amino acid?
Its side chain can shift between a positive and neutral charge, depending on the pH, making it important for enzyme active sites
T or F: During translation, the C-terminus of any protein is the first amino acid in the chain and subsequent amino acids are added to the amide end, the right hand end of the growing chain
False, the N-terminus is the first!
The number of different polypeptide sequences is limited by two factors?
1) 20 amino acids
2) The number of amino acids found in that polypeptide (20^n)
What factors drive protein folding?
Ionic bonds, hydrogen bonds, Van der Waal forces, hydrophobic effect
What is the hydrophobic effect?
The tendency of non-polar amino acids to aggregate in the protein interior to minimize exposure to water
How do hydrogen bonds contribute to protein structure?
They help stabilize secondary structures like alpha-helices and beta-sheets
How are alpha helices and beta sheets stabilized? What’s the primary difference?
They are both stabilized by hydrogen bonding between carbonyl groups (O) and amide groups (H)
Alpha Helices: hydrogen bonds form within the same polypeptide strands, four residues apart from each other
Beta Sheets: hydrogen bonds form between adjacent polypeptide strands or within a singular polypeptide (parallel or anti-parallel)
T or F: Alpha helices and beta sheets can vary in hydrophobicity, either being predominantly hydrophobic, hydrophilic, or even sometimes amphipathic
True
What are beta turns and why are they important?
They are a type of connector that often supports beta sheets, they usually involve 3 or 4 amino acids residues, they’re short loops stabilized by hydrogen bonding that allow a polypeptide to change direction
What are examples of common motifs?
Coiled-coil: two alpha helices (EX: leucine zipper, commonly found in DNA binding proteins, can fit in grooves of DNA helix)
Zinc-finger: alpha helix and 2 beta strands, stabilized by a zinc ion (EX: C2H2, C4, C6, cysteine and histidine, commonly found in DNA binding proteins, also RNA)
Beta-barrel: a sheet forming a cylindrical structure (four to ten anti-parallel strands, useful to form a channel across a membrane, amphipathic, hydrophilic core)
Helix-loop-helix: two alpha helices, connected by a loop, and co-factor (calcium)
What is a protein domain?
A substructure of a polypeptide that can fold independently into a stable structure, they can either be functional or structural domains
What is a dimer? What is the difference between a homodimer and a heterodimer?
A dimer would refer to a complex consisting of two polypeptides or two subunits associated together. A homodimer has two identical polypeptides and a heterodimer has two different polypeptides
T or F: The stable conformation of a protein cannot be achieved until its actually interacting with its substrate, so recognizing the substrate and stabilizing the protein occur together.
True
Explain the following: acetylation, methylation, phosphorylation, hydroxylation, carboxylation, glycosylation, and lipidation
Acetylation: adds an acetyl group, protects against degradation
Methylation: adds a methyl group, modifies protein interactions
Phosphorylation: adds a phosphate group to serine, tyrosine, and threonine using kinases, the opposite is conducted by phosphatase
Hydroxylation: adds a hydroxyl group
Carboxylation: adds a carboxyl group, adds a negative charge
Glycosylation: adds carbohydrate, occurs in the Golgi apparatus
Lipidation: adds lipid molecules, anchors proteins to membranes
Three Rules of Protein Folding
First proposed by Christian Anfinsen based on his study of the ribonuclease A protein
1) Spontaneous
2) Reversible
3) Unique
List examples of hereditary disorders and prion-based diseases that result when proteins misfold
Hereditary disorders: cystic fibrosis, Emphysema, Alzheimer’s disease
Prion-based diseases: Creutzfeldt-Jacob disease, Mad Cow disease
