eLa Online Assignments Flashcards
What is roughly the pKa of Asp/Glu sidechain residues?
They are roughly 3.5-4.0
What is roughly the pKa of Lys/Arg residues
10.5-12.5
What is the pKa of histidine?
pKa - 6.1
What is unique about glycine in regards to proteins?
Glycine has a small sidechain so proteins can adopt a wide array of conformations and are considered flexible
What is unique about proline in regards to proteins?
Very rigid and tends to form kinks in the protein
Not often found in alpha helicies and B-sheets
What are unique about cysteine residues in regards to proteins?
Cys residues can form disulfide bonds with each other
This is the only common covalent bond that is formed between sidechains
What are the non covalent interactions of amino acids
Ionic Interaction, hydrophobic interactions, hydrogen bonds
What is an noncovalent ionic interaction?
Charged molecules may be interacting with other opposite charged molecules
Aspartic acid interacting with lysine
What are noncovalent hydrophobic interactions?
Hydrophobic side chains that group together. Usually toward the center of the protein
What are noncovalent hydrogen bonding?
H-bonds can form whenever a strongly electronegative atom approaches a hydrogen atom
What is a strong acid?
An acid that completely dissociates in water
What is a weak acid or base?
Weak acids or bases do not completely dissociate in water, thus they are give characteristic dissociation constants to describe their behavior
What is the definition of pH?
pH is defined as the negative logarithm of the concentration of H+ in solution
What is the Ka of a solution?
Ka is the acid dissociation constant of a weak acid
What is pKa?
-logKa
What is a buffer?
Buffer is a solution containing and acid and its conjugate base that is resistant to large changes in pH
What is buffer capacity?
A quantitative measure of the resistance of a buffer solution to pH change
What does the henderson-Hasselbalch equation describe?
The equation describes the relationship between the pH of a solution and the relative amounts of a conjugate pair in that solution
How does the body compensate for changes in acid-base status?
Weak inorganic acids are especially critical for buffering biological fluids. The phosphate system helps buffer the cytoplasm
At what pH would serine have a fully pronated side chain?
At pH of 2.0, the lower the pH the more H+ ions present that will attach itself to the side chain
Why is SDS-PAGE more appropriate for electrophoresis of integral membrane proteins than native gel electrophoresis?
The detergent nature of SDS prevents aggregation of the membrane proteins that might occur in a native gel
What does having a high membrane:volume ratio and biconcave shape allow the erythrocyte to do? Where does this shape come from?
The biconcave shape allows for the erythrocyte to be flexible. The extra membrane allow them to squeeze into small capillaries. The shape comes from the attachment of the plasma membrane to the cytoskeleton.
What type of filament does actin form?
microfilament
Sphingomyelin is what type of membrane lipid?
Phospholipid
What important distinguishing feature are on the outside of the RBC?
ABO an Rh systems
How could you describe the permeability of a RBC to water? How must this be taken into account when formulating IV mixtures?
An RBC is highly permeable to H2O due to the presence of aquaporins. When formulating IVs they must contain the same level of solutes as inside the cell.
What would comprise a hypotonic IV solution?
More water and less salt than the cytoplasm of a normal erythrocyte
What would comprise a hypertonic IV solution?
More salt and less water than the cytoplasm of a normal erythrocyte
What are characteristics of hereditary spherocytosis?
Improper sodium transport and decreased membrane to cell volume ratio. Defects in the proteins that connect the membrane to the cytoskeleton
How are defects detecting a expression levels for RBC membrane proteins?
Changes to the SDS-PAGE
What is an elliptocyte?
RBC has an elliptical shape resulting from mutations in alpha or beta spectrin
Phospholipids are a derivative of what?
glycerol or sphingosine
Glycolipids are derived from what?
sphingosine
What is a feature of cholesterol?
Plasma membrane embedded cholesterol creates kinks in the PM making it less fluid and more rigid
What are amphipathic lipids?
Lipids that contain a hydrophobic and hydrophilic portion
What are peripheral proteins?
proteins that sit on the membrane that are anchored by a nonpolar moiety
Does altering the substrate concentration change the Km?
NOOO
Where would you ideally have the Km of an enzyme so that it is primed to react to levels above the norm?
The Km would sit right at the top of the normal levels so it could still respond to higher levels
What is a thiol?
It is an organosulfur product
Cells have a high intracellular concentration of what positively charged ion?
Potassium
Cells have a high extracellular concentration of what positively charged ion?
Sodium
A large pore is inserted into the membrane of an RBC. What would be a possible result of this?
A large amount of unregulated Na+ influx
What protein family includes claudin?
Zonula occludens
What types of bonds to lyases break?
C-C, C-O, C-S, C-N
In cases of starvation, what are some major metabolic changes?
The brain uses ketones for fuel
The liver derives it energy from breakdown of fatty acids
Muscle proteins are broken down
Fat in adipose tissue is broken down
Do RBCs use ketone bodies for energy?
No because they have no mitochondria
What does alpha-spectrin do?
Links the plasma membrane to the cytoskeleton
What does fibronectin bind?
It bind integrin and type 4 collagen
What is the use of Kalydeco?
It is a potentiator. It needs existing pumps to exist, it does not create new ones
Where is the steady state
It is the point before the equilibrium, before the rate has hit vmax and is in eq
Why are desmosomes said to contain plaques?
Some components bind heavy metals more tightly
What is the organization of the basement membrane?
Entactin will bind to collagen and laminin to bind these sheets together.
Fibronectin will bind to collagen and to integrins on the cell surface.
What do proteoglycans do in the basement membrane?
Proteoglycans will bind to laminin and to the dystroglycan complex. They also act as signalling molecules, and can bind and present other growth factors.
Phenelzine inhibits MAO irreversibly while tranylcyclopromine binds to MAO reversibly. What can be said about the length of time they are in a system?
The effects of phenelzine will last weeks while Tran will last a few days
What is hypertrophy?
Increased size of cells
Why are desmosomes prominent on the skin?
The skin suffers shear stress moreso than other organs
Will the stomach ever exist at equilibrium?
No, it is constantly emptying its contents into the small intestine
Will a warm or cold temperature speed up reactions?
Warm
Why can epidermolysis bullosa be such a serious threat?
Blistering occurs in the junction between the cell and the basal lamina allowing for access by pathogens
What does a case control study start with?
It starts with a disease
What is a ceramide?
a sphingosine and fatty acid
What is a cerebroside?
A common name for a group of glycosphingolipids
How does type 4 collagen contribute to the kidneys?
Contributes to the filtration barrier created by the basement membrane of the glomeruli in the kidneys
What motor protein is going to be found in the periphery?
Dyenin - brings back cargo so it would be in high concentrations in the periphery
What is an epitope?
Region of antigen that binds directly with antibody
What are the two types of antibodies that can be used in ELISA and what are the characteristics of each?
Polyclonal - mixture of Ab, may recognize different epitope, each would have different binding affinity and may experience cross-reactivites
Monoclonal - unique Ab created by cloning a cell line much more uniform response
What is the basic protocol for ELISA and what is the difference with RIA?
Antibody is fixed to bottom of plate and antigen is introduced into the test. Antigen binds to antibody. Wash away anything that doesnt bind. Recognition of antigen by another antibody. This antibody is used for detection. RIA is involved in radiolabeling so it works much better at low concentrations
What is the difference between sandwich and competitive ELISAs?
Sandwich refers to using more than one antibody in order to detect. Antigen should have more than one binding site. Competitive works best with one epitope and the less of a color change determines that more antigen is bound to antibody.
What are two factors that can limit ELISA and RIA activity?
More antigen can be present than available Ab
Cross-reactivity may lead to false positives
What happen within the first 10 minutes of ischemic conditions?
O2 is depleted in the first few seconds
Ox Phos comes to a screeching halt
Citric acid cycle continues to generate products that are sent to Ox phos. abortive ox phos results in high levels of free electrons
Cells will generate ATP via glycolysis but will stop once glucose stores are exhausted.
How does ischemia affect ion gradients?
Na+,K+ ATPase uses ATP for primary active transport to maintain Na+ and K+ ion gradients
Ion gradients that are central to nerve function will lose function within 5-10 minutes.
Calcium ion gradients are also severely altered which can lead to nerve cell death via apoptosis
What type of oxidative damage can occur that results from ischemia and reprofusion?
Acivation of phospholipase A2 releases archadonic acid for further metabolism to signaling molecules leading to increased free radicals and ROS
Activation of NOS leads to increase NO with can react with superoxide to form peroxynitrate the reacts further to form NO2 and hydroxide radical
Xanthine oxidase is dangerous upon reprofusion why is this?
Xanthine oxidase, once reprofusion occurs, reacts to form H2O2 twice and urate molecules
