Unit 1: Cells & Membranes
Why is water capable of forming hydrogen bonds with the major macromolecules?
The hydrogen atoms carry partial positive charges.
The oxygen atom carries a partial negative charge.
It is a polar molecule.
The hydrogen atom is less electronegative than the oxygen atom.
All of the above apply.
5
Which linkage forms the backbone of a nucleic acid?
A Sugar-phosphate linkage
The leading strand is the daughter strand that has its ____ end pointed toward the replication fork and is therefore synthesized ______.
3’; continuously
Define anabolism and catabolism. How is energy involved in these processes?
Anabolic reactions involve the building of larger, complex molecules from smaller, simpler ones, and require an input of energy. Catabolic reactions break the chemical bonds in larger, more complex molecules and release energy.
What is the strongest type of non-covalent bond that the polar amino acid side chains can participate in with each other?
Permanent-dipole – Permanent-dipole
Prokaryotes and eukaryotes have evolved different cellular strategies as cells.
What are some differences between these types of cells? What characteristics could you use to distinguish between them?
Prokaryotic cells have no membrane bound compartments; Eukaryotic contain a nucleus surrounded by a nuclear envelope, and many membrane-bound compartments, such as mitochondria and (in plants) chloroplasts.
Alternate correct answer: test if chromosome is linear or circular
What specific sequence or region leads to transcription termination and translation termination?
The terminator sequence mediates transcription termination.
Translation is terminated by the stop codon.
What catalyzes DNA synthesis?
DNA polymerase
Glycolysis involves an energy investment phase, cleavage phase, and an energy pay-off phase. For every glucose molecule that enters the glycolytic path, what is the number of ATP used; the number of ATP produced; and the net ATP yield at the end of glycolysis?
2, 4, 2
You make single amino acid changes in the GDP-binding pocket of the G protein shown in the figure above, and examine their effects on the binding of GDP. Consider the nature (e.g. charge, polarity, hydrophilicity, hydrophobicity) of the amino acid side chains and give the most likely reason why each of the amino acid changes has the stated effect.
Consider each amino acid change independently.
Arg is changed to a Lys, resulting in a G protein that still binds GDP.
Lys is changed to a Glu, resulting in a G protein that cannot bind GDP.
1. Lys is +vely charged (just like Arg) and likely did not change the interactions in the region much.
2. Glu is –vely charged and this would lead to charge repulsion with Phosphate of GDP – which is likely preventing GDP from binding to G-protein.
What is the most important factor explaining the spontaneous assembly of phospholipids into a bilayer in an aqueous solution?
Increased entropy of water, and thereby the stability of the system
What determines where the E. coli RNA Polymerase initiates transcription?
The binding of the sigma subunit to the DNA binding sequences upstream of the transcription start site.
A defect occurs during replication where DNA replication proceeds without the RNA primers being removed and replaced with DNA. Which enzyme is most likely to be defective in this system?
A DNA polymerase (technically DNA Polymerase I)
What electron carrier(s) function in the TCA cycle?
both NAD+ and FAD
One of the reasons that scientists grow bacteria in a cell culture is to clone genes. You have successfully cloned your gene into E. coli and you want to grow a big batch, so you can extract the most DNA possible. When should you harvest your cells to do the DNA extraction?
Between exponential and stationary.
Which of the following statements is true about passive diffusion?
Passive diffusion operates independently of concentration.
Passive diffusion phenomena can never reach equilibrium.
Passive diffusion requires no expenditure of cellular energy.
Passive diffusion moves molecules into a cell, but not out of the cell.
Passive diffusion does not occur in cells that possess a cell wall.
C
If a given tRNA has an anticodon of 5’-ACU-3’, what is the mRNA codon, what is the template strand DNA sequence, and which amino acid does it carry?
tRNA 3’ UCA 5’ or 5’ ACU 3’
mRNA: 5’- AGU-3’ or 3’-UGA-5’
template strand: 5’-ACT-3’ or 3’-TCA-5’
Amino acid: Ser
Put the following steps of DNA replication on the lagging strand in chronological order.
A. Single-stranded binding proteins attach to the DNA strands.
B. Hydrogen bonds between base-pairs of the DNA strands are broken.
C. Primase binds to the single strand DNA.
D. DNA polymerase elongates the primer.
E. A short RNA primer is created.
B, A, C, E, D
What is the difference between NADH and NADPH?
Both function as electron carriers, but NADPH has an additional phosphate group compared to NADH.
Consider the basic structure of an operon. Each protein coding sequence within that operon would have:
1. Its own promoter.
2. Its own transcription terminator.
3. Its own start codon.
4. Its own stop codon.
3 and 4
You are given the amino acid sequence of a protein. All 20 of the common amino acids are present in the protein. When you know the amino acid sequence, what can you predict about the final conformation this protein will assume (choose all that apply)?
1. If this protein will form a quaternary structure
2. Whether secondary structures like alpha helices will form within the protein.
3. If, in the 2o structure, a disulphide (S-S) bond will form between 2 cysteine residues.
4. If this protein contains transmembrane domains through the lipid bilayer.
2 and 4*
*Part of the sequence of this polypeptide chain would have hydrophobic side chains in order exist through the lipid bilayer i.e. in part, interacting with lipid tails.
Not all mutations in a protein coding region cause a change in phenotype. Explain giving 2 examples.
Example: If it’s a silent mutation (i.e. one codon changes to another codon coding for the same amino acid) there will be no change in phenotype because there is no change in the shape or function of the protein. then you must add that there is no change in the polypeptide and/or no change in the shape and function of the protein.
Example: If there is a missense mutation and the amino acid that is swapped in is of a similar type (similar non-covalent interactions are possible, the size is similar) this means protein folding and function is less likely to be affected.
Describe three major challenges faced by both bacteria and eukaryotic cells in replicating their DNA, and how the challenges are overcome.
Challenge 1: Strand separation – separation of the double stranded DNA by breaking the H-bonds, to allow DNA Pol to bind to the single-stranded template DNA and synthesize the complementary daughter strand. This is achieved by specialized proteins (enzymes) called Helicases.
Challenge 2: DNA Polymerase needs a primer to start synthesis – dealt with by the enzyme RNA Polymerase (Primase) synthesizing RNA primers that the DNA Pol can use to extend.
Challenge 3: DNA replication machinery makes mistakes introducing mutations – dealt with by having proof reading capacity and DNA repair machinery.
In photophosphorylation, what is the role of water (H2O)?
It donates electrons to replace lost electrons in the reaction center of photosystem II.
Which of the following statements about regulation of the lac operon of E. coli are correct? CHOOSE ALL THAT APPLY
A. The LacI protein binds to the operator and inhibits transcription of the lac operon.
B. When grown in media with no lactose, E. coli produce high levels of lacZY mRNA.
C. The LacI protein will change shape in the presence of lactose.
D. Cells that contain a mutant LacI protein that cannot bind lactose are unable to metabolize lactose.
E. When cells are grown in medium that contains lactose, the LacI protein, after binding to lactose, will bind near the promoter for the lac operon.
A, C, D