Chapter 5 Flashcards
What type of reaction forms amino acid chains?
Condensation Reaction
What type of bond holds together amino acids?
Peptide Bond
How are peptides read?
N-terminus to C-terminus
How are amino acid chains named?
Drop “-ine” from amino acid and add “-yl”
What was the first protein to be sequenced?
Insulin
What are the units for Daltons?
g/mol (atomic mass unit)
What holds amino acid chains together?
Disulfide Bridges
What is an isopeptide bond?
Amide bond that includes carboxylic acid or amine that isn’t from the backbone (comes from the side chain)
What is the issue with trying to determine protein sequence from corresponding DNA?
Not all DNA is translated into amino acids
What technique separates all amino acids?
Acid hydrolysis
Are protein subunits held together with strong or weak forces?
Weak
What are the four ways to separate protein subunits?
- extreme pH
- 8M urea
- 6M guanidine HCl
- High Salt Concentration
How do 6M guanidine HCl and 8M urea cause protein separation?
Associate with protein and replace hydrogen bonds
What is used to reduce disulfide cross-bridges?
2-Mercaptoethanol
How does 2-mercaptoethanol reduce disulfide bonds?
Reduces disulfide bridge to thiols
What do you need to be careful of when using 2-mercaptoethanol to reduce disulfide bridges?
Deprotonating the resulting thiols
What amino acid is the most common to form disulfide bridges?
Cystine
What is used to prevent (block) the reformation of disulfide bridges?
Iodoacetate
What side of the peptide bond does trypsin cut on?
Right (C-terminus side)
What side of the peptide bond does chymotrypsin cut on?
RIght (C-terminus side)
What side of the peptide bond does elastase cut on?
Right (C-terminus side)
What side of the peptide bond does thermolysin cut on?
Left (N-terminus side)
What side of the peptide bond does pepsin cut on?
Left (N-terminus side)
What side of the peptide bond does endopeptidase V8 cut on?
Right (C-terminus side)
What is the specificity of trypsin?
R(n-1) = Arg, Lys
Except: R(n) = Pro
What is the specificity of chymotrypsin?
R(n-1) = Phe, Trp, Tyr
Except: R(n) = Pro
What is the specificity of elastase?
R(n-1) = Ala, Gly, Ser, Val
Except: R(n) = Pro
What is the specificity of thermolysin?
R(n) = Ile, Met, Phe, Trp, Tyr, Val
Except: R(n) = Pro
What is the specificity of pepsin?
R(n) = Leu, Phe, Trp, Tyr
Except: R(n) = Pro
What is the specificity of endopeptidase V8?
R(n-1) = Glu
What hydrolyzes on the C-terminal side of a methionine?
Cyanogen Bromide Hydrolysis
What does carboxypeptidase function for in the sequencing of polypeptides?
Hydrolysis of the C-terminal amino acid
What does dansyl chloride do in the sequencing of polypeptides?
Determines the N-terminal amino acid, but destroys the rest of the polypeptide in the process
What does the Edman reagent do in the sequencing of polypeptides?
Determines the N-terminal amino acid, while leaving the rest of the polypeptide intact
What is the primary means of protein identification?
Mass Spectrometry
How does mass spectrometry separate proteins?
Based on the mass-to-charge ratio
What is a protein domain?
Highly conserved amino acid sequence often with a conserved function between proteins
What is the difference between a polymorphism and a mutation?
Polymorphism - relatively common natural variation, usually conservative and benign
Mutation - uncommon change, usually non-conservative, and may be detrimental
What is a homolog?
Proteins that are evolutionarily related
What is an ortholog?
Homologous proteins with the same function in different species
What is a paralog?
Homologous proteins created from a gene duplication
What does SDS do?
Binds to hydrophobic interactions in proteins and prevents refolding
What is the function of beta-mercaptoethanol?
Reduces disulfide bridges
What chemicals disrupt hydrogen bonding?
Urea and Guanidinium
What is homogenization?
The process of breaking open cells
What chemical is used to target cell walls?
Lysozyme
What is used to disrupt the lipid bilayer?
Detergents (ex. SDS)
What are the three ways of quantifying protein in solution?
UV
Bradford
BCA Assay
What UV do proteins absorb light at? Which amino acids do this?
280nm
Amino Acids with rings (Tyr, Trp, Phe)
How does a Bradford assay work?
Binding of a dye to hydrophobic areas of protein to create blue color change
What absorbance is a Bradford assay read at?
595nm
What limits Bradford assays?
Detergents
How does a BCA assay work?
Reduction of Cu(2+) to Cu(+) by protein backbone. BCA turns purple with Cu(+) but not Cu(2+)
What absorbance is a BCA assay read at?
562nm
What limits a BCA assay?
Reducing agents
What protein purification technique is used to sort by solubility?
Salting Out
What is the eluent of chromatographic purification?
Molecules released from the column during separation
How does ion exchange chromatography separate molecules?
Based on charge
Cation/Anion in the stationary phase that binds to the opposite
What is the difference between a strong and weak resin?
Strong resin will always have its charge; weak resin will change its charge based on pH
How does gel filtration chromatography separate molecules?
Based on size
Larger molecules then smaller molecules
How does affinity chromatography work?
Small ligands are attached to the matrix that binds to the protein of interest. Protein is then eluted with a high concentration of the free ligand.
How does SDS-PAGE separate proteins?
Based on size
How does two-dimensional gel electrophoresis separate molecules?
First separated by isoelectric focusing (x-axis), then separated by size (y-axis)
