Thermodynamics, Water, & Buffer
What is the ideal range of a buffer's pKa compared to the pH of the buffer solution?
pKa plus/minus 1 pH
Name the 3 types of chromatography used to separate protein
Gel filtration (size exclusion), ion exchange, affinity
Common AAs (2) used in beta turns
Proline (Type I) and glycine (Type II)
Type of model that antibody-antigen binding follows
Induced fit
Polymer and monomer of actin
F-actin, G-actin
Equilibrium constant number of water, Kw
Kw=10^(-14)
Which amino acid is less frequently observed in alpha-helices and why?
Proline; unique backbone makes it too rigid
What are the torsion angles of protein and between what atoms are each angle?
Phi = ɸ is between alpha-carbon and N
Psi = Ѱ is between alpha-carbon and C of COOH
Branches (2) of adaptive immunity. What type of immune cell is most prevalent in each of the 2 branches?
Humoral and cell-mediated; B vs T lymphocytes
Region of a sarcomere that:
a) Contains only actin filaments
b) Contains both action and myosin filaments
c) Contains only myosin
a) I (isotropic) band
b) A (anisotropic) band
c) H-zone
Order from middle to end of sarcomere: Hai 👋
Indicate the false statements and WHY:
a) Enzymes can lower the activation energy of a reaction and change delta G.
b) Enzymes can change the rate of reaction.
c) Enzymes can stabilize the transition state of a reaction.
"a" only (can't change delta G/spontaneity)
Purpose of reducing agents (beta-mercaptoethanol or DTT) used in SDS-PAGE
Break covalent disulfide bonds
Name two chaperone proteins that use ATP. What do chaperones do in assisting with protein folding?
Hsp70/Hsp40 (Hsp70 is the chaperone, Hsp40 is the cofactor that helps deliver the unfolded protein to Hsp70)
GroEL/ES
Unfolded protein binds GroEL.
GroES binds, forming a “folding chamber.”
ATP hydrolysis drives folding inside the cavity.
GroES and folded protein are released.
Chaperone proteins shield hydrophobic side chains of folding proteins.
Name all 5 types of immunoglobulins. Which one is first made by the body to fight a new infection?
GAMED; M
What regulatory proteins work together to block myosin-binding sites on actin? The release of what from what organelle causes this complex to move, exposing the myosin-binding sites?
Troponin and tropomyosin; Ca++, sarcoplasmic reticulum
If a process can occur spontaneously at low temperature, but not at high temperature, is the process ENDO/EXOTHERMIC and what sign is the entropy?
Exothermic (negative delta H) and a negative entropy (delta S)
Which ones are TRUE?
a) Edman degradation (ED) can only work with large proteins.
b) One downside of ED is that errors that occur early on can compound over multiple cycles
c) MS-MS (tandem MS) can be used to detect protein modifications
d) Single MS can be used to detect the exact protein sequence
a) False, best for small proteins
b) True
c) True
d) False, only for MS-MS. Single MS gives protein mass only
Conclusions (3) drawn from the classic Anfinsen experiment about protein folding (experiment involved treating a protein with ribonuclease + reducing agent and seeing what happens after both reagents are removed)
1. Protein folding is spontaneous (delta G < 0)
2. Protein folding is reversible (to some extent).
3. Protein folding is determined by 1* structure.
IgG has how many hypervariable regions on EACH arm? How many in total?
6; 12
Differences between Fast Twitch and Slow Twitch muscle fibers (list as many as you can)
Fast: (sprinters), exhaust quickly, anaerobic respiration (direct phosphorylation, glycolysis, and lactic acid formation), fewer ATP generated but more quickly, Type II muscle fibers, Myosin with faster ATPase rate, Larger
Slow: (marathon runners), aerobic respiration, 38 ATP per glucose lasting for a longer period, Type I muscle fibers, Slow ATPase rate
H2CO3 --> H(+) + HCO3(-)
If additional H(+), when the reaction reaches equilibrium again, what will happen to the concentration of the conjugate base of carbonic acid and the concentration of carbonic acid?
Decreases; increases
H(+) increases so reaction will shift to left to make more reactants
Name:
5 nonpolar AAs
All polar ones
All + charged ones
All - charged ones
Which one can have their sidechain be modified
---
Ser, Thr, Tyr, Asparagine, Glutamine
Lysine, Histidine, Arginine
Aspartic acid & glutamic acid
Lysine
Indicate the FALSE statements:
a) All proteins have domains, which provide the functions of the proteins
b) Proteins are folded locally first, by specific order, one initiation site after another
c) Protein folding often contains many local minima traps
d) Hydrogen bonds play the most important role in protein folding at the 3* and 4* levels
a) False, not all proteins have domains
b) False, can occur through multiple parallel pathways
c) True
d) False, hydrophobic interactions do for 3* and 4* (H-bonds are most important for 2*)
What are the individual advantages of Hapten and Carrier molecules that make the Hapten-Carrier conjugate so potent in triggering immune responses?
Hapten: small (also a disadvantage) and specific
Carrier: big, easily recognized
HC conjugate: big AND has specificity
a) Binding ATP
b) Hydrolysis of ATP into ADP and Pi
c) Release of ADP and Pi
a) Myosin releases F-actin (relaxed state)
b) "Cocked", releasing energy for contraction
c) Power stroke (myosin remains attached until a new ATP is bound)