CH 4 Flashcards
Maintaining pH and salt concentrations is critical to keeping proteins functional. What is the molecular mechanism by which pH affects protein function?
A few of the polar R-groups can change charge, and the new attraction or repulsion can alter the shape of the protein
To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process?
The solvents break some to most of the noncovalent interactions, resulting in a misfolded protein.
what amino acids form disulfide bonds
cysteine amino acids
makeup of an amino acid
central carbon, amine group, carboxylic acid, and side chain R group
Molecular chaperones can work by creating an “isolation chamber.” What is the purpose of this chamber?
This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.
Why is it necessary to fully denature polypeptides (including breaking disulfide bonds) to accurately separate proteins on the basis of size in an SDS-PAGE gel?
disulfide bonds and protein folds would alter the migration of polypeptides.
Michaelis-Menton curve
point where enzyme rate is maximized with high substrate conditions
Which of the following best describes the molecular mechanisms in which lysozyme lowers the energy required for its substrate to reach its transition-state conformation?
by altering the shape of the substrate to mimic the conformation of the transition state
Studies conducted with a lysozyme mutant that contains an Asp→Asn change at position 52 and a Glu→Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant?
These amino acid substitutions will change the shape of the protein in the active-site scaffold.
In some cases, small molecules are integral to the function of enzymes and are dubbed “coenzymes.” Which of the following is a coenzyme for the enzyme carboxypeptidase?
zinc
The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in. …
protein degradation
Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. As the relative amount of ADP molecules increases, ADP can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is …
allosteric activation
Elastin molecules
help bendy-flexible properties for structure
Disulfide bonds are stronger than…
hydrogen
Acidic
O-, lost a proton
Basic
O+, gained a proton
How antibodies defend
Form aggregates and then are ingested by phagocytic cells
Lysozyme
antibiotic enzyme
attacks polysaccharide chains of bacterial cell wall
Allosteric enzymes
have two or more binding sites that influence eachother
GTP binding proteins on/off
turned on and off by gain and loss of phosphate group
What drives motor protein movement
ATP hydroylsis
many interacting proteins are brought together by…
scaffolds
Many amino acids are made from…
other amino acids
Orthosteric inhibitation
Inhibitor binds to active site
Allosteric inhibitation
inhibitor binds to regulatory site (not active site) that changes shape of active site
Kinase vs Phosphatase
Kinase adds Phosphate group
Phosphatase removes
Scaffolds
Similar to enzymes, bring many proteins together to make a protein complex
Homogenization
methods to rupture plasma membrane to empty contents
Homogenate
soup or extract left over from homogenization that contains small molecules and organelles from the cytosol
Supernatant
less dense portion of molecules and liquid from centrifuge above denser parts
Column chromatography
method to filter proteins, can be separated by
-charge
-hydrophobicity
-size
-ability to bond to certain groups
3 types of chromatography
-ion exchange
-gel-filtration chromatography
-affinity chromatography
Ion exchange Chromatography
column packed with small beads carrying either positive or negative charges to retard opposite charge proteins. Matrix depends on PH and ionic strength of solution
Gel filtration Chromatography
columns separate based on size, hollow beads allow smaller proteins to envelope and allow larger proteins to pass through
Affinity Chromatography
Matrix has molecules that bind to protein of interest, they can be released by pH change or conc. salt solutions
-highly pure
Electrophoresis
electric field in a protein solution causes proteins to move based on their size and charge
Isoelectric focusing
electric field gradient applied to filter proteins based on their isoelectric points
Isoelectric point
pH point where protein has no charge and wont move in an electric gradient
two-dimensional polyacrylamide-gel electrophoresis
can resolve more than 1000 proteins in a 2d map
-separated top to bottom by atomic weight
-separated left to right by pH
X-Ray crystallography
first 3d images of proteins, protein is coaxed to from crystals
Storage proteins
store ions or amino acids
Transport proteins
transport small molecules or ions
