Chemistry & thermodynamics
Which atoms can form hydrogen bonds with H?
N, O, F
List 3 differences between DNA and RNA
RNA: ribose (-OH), uracil, single-stranded
DNA: deoxyribose, thymine, double-stranded
What is needed in order for aminoacyl-tRNA synthetase to bind a tRNA to an amino acid and why?
ATP hydrolysis because it requires energy to form covalent bond
What brings transmembrane proteins to the ER membrane?
SRP and SRP receptors (SRP recognizes and binds to transmembrane region on polypeptide being built by a ribosome, and pulls the ribosome and the polypeptide to the membrane by binding to SRP receptor on the membrane)
What is the difference between the minus and plus end of an actin filament?
ATP vs. ADP bound
A strong acid has a __(high/low)___ pKa and is ___(protonated/deprotonated)___ in a neutral solution
low, deprotonated
Two amino acids that can’t form an alpha helix?
Glycine (achiral; too flexible) and proline (imino acid; causes kinks)
How does RNA polymerase know where to start transcription in bacteria? Be specific.
-35 and -10 on promoter
Difference between primary and secondary messengers & example of each
Primary: ligands (eg adrenaline), secondary: amplifies signals inside cell (eg cAMP)
What keeps chromosomes attached to microtubules during mitosis?
Kinetochores (Dam 1 complex)
Why is ATP considered a high-energy molecule?
The phosphoanhydride bonds (connecting the phosphate groups) are unstable and can be easily broken and reattached to other molecules, releasing energy
Name the basic amino acids, and draw them on the board
Lysine, Arginine, Histidine
RNAse, DNA polymerase I, ligase
What “players” in nuclear import are found on both sides of the membrane?
Importin, Ran
Where does microtubule nucleate from inside the cell?
Centrosomes (y-tubulin ring complexes)
Give an example of indirect coupling, and explain how does it work?
DNA synthesis. The rapid breakdown of PPi drives the addition of a dNTP to the growing DNA strand
Define the 4 levels of protein structures, and what is the special bonding that only occurs in tertiary and quaternary structures?
Primary: linear sequence of amino acids
Secondary: local folding patterns (a-helix, b-sheet)
Tertiary: 3D comformation of a single polypeptide chain
Quaternary: arrangements of multiple polypeptide chains
Disulfide bonds
Name 3 common mutations that occur after replication. By what method can these be repaired?
Depurination, deamination, thymine dimers
mismatch repair
Which step in the membrane fusion process which requires ATP and what would happen if it didn't take place?
Unwinding of v-SNARE and t-SNARE. If they were not separated using energy from ATP, future vesicle fusion would stop because there would eventually be no free v-SNARE and t-SNARE
Walk through the steps of myosin movement.
Attachment -> released -> cocked -> force-generating -> attachment
Aspartic acid - Methionine - Glutamic acid - Serine - Lysine
What is the net charge of this peptide bond at pH = 7?
-1
Draw the basic structure of a peptide bond. Why peptide bonds can't rotate?
Partial double bond property, got from resonance.
What is the difference between EF-Tu and EF-G?
EF-Tu: GTPase that catalyzes binding of aa-tRNA to ribosome
EF-G: GTPase that moves ribosome over by one codon
What would be the consequence to nuclear import if a mutation in RAN-GEF caused it to lose its affinity to chromatin?
The gradient of Ran-GTP and Ran-GTP would be lost because RAN-GEF could cross into the cytoplasm and convert Ran-GDP back to Ran-GTP, and nuclear import would stop working.
What would happen if there was a mutation in Wee1? Cak? Cdc25?
Wee1: smaller cells because division happens prematurely
Cak: longer cells because no activating phosphate
Cdc25: longer cells because inhibitory phosphate can’t be removed