BIOL 3090 Sect.

1 (DiMario); Spring, 2020

Study Guide for Exam 1

Our first test is on Wed. Feb. 5. Everything we covered in lecture and all reading assignments
are fair game, but this review/study guide covers topics that I feel are most important. The material from
lecture 9 on Monday, Feb. 3 lecture will not be on the exam. We’ll save it for the second exam.

Use the study guide as a check list; once you know one topic, move on to the next. Pace yourselves.
After the study guide, there are some sample questions to give you an idea of depth of knowledge, and a
stern warning about using old exams as your only study tool.

Chapter 1, Molecules, Cells, and Model Organisms

1) What are the four aspects of the cell theory.
2) Archaea are in between prokaryotes and eukaryotes in terms of evolution (Fig. 1-1).
3) Halophiles vs. Thermophiles vs. Methanophiles
4) What is the nucleoid in a prokaryotic cell (Fig. 1-11)?
5) What important internal features distinguish eukaryotic cells from prokaryotic cells?
6) List the names and functions of the various eukaryotic organelles (Fig. 1-12b). Would you consider
the nucleolus inside the nucleus an organelle?
7) What are the three components of the cytoskeleton (Fig. 1-13), and what proteins make up these
components?
8) Review the model organisms and what features each organism is good for.
9) What’s an ES cell, what features does it possess in terms of mammalian development, and why is it in
the news? How do you obtain ES cells?
10) Of the principal macromolecules, which has the most diversity in terms of structure and function?
11) What macromolecule would you say indirectly regulates the synthesis of all other macromolecules?
12) Review the eukaryotic cell cycle. What’s G0? Roughly, what percentage of the cell cycle is mitosis?
(1/20)

Chapter 2, Chemical Foundations

1) Differences in Electronegativity to explain:
polar versus non-polar covalent bonds
ionic bonds
hydrogen bonds
2) van der Waals and hydrophobic interactions. (Figs. 2-10 and 2-11 are good).
- Why are transient bonds important for the cell?
3) Reaction rates and chemical equilibrium. Why is the Kd useful in Cell Biology/Biochemistry?
4) Know your milli, micro, nano, and pico Molar scales. At what Kd range do most biochemical
interactions occur?
5) The difference between true equilibrium and steady state.
6) Definition of pH, both the little mathematical formula for pH, and what the formula means.
7) Henderson-Hasselbalch equation, and what it means regarding biological buffers (pKa). When does
the pKa = the pH? What is the middle pKa of phosphoric acid, and why is that one so important?
8) Positive/negative ΔG's and coupled reactions. ATP hydrolysis to drive coupled reactions forward.
9) What is the activation energy? What does a catalyst do for a reaction that has a favorable –ΔG? What
does a catalyst not do?

Chapter 3: Protein Structure and Function

1) Know the 20 standard amino acids and their three letter abbreviated names.
 T/F: Right-handed (D) amino acids make up proteins.
2) Which amino acid forms disulfide bonds? Why are Pro and Gly “special”?
3) What happens when you: acetylate the side chain of Lysine (Lys); phosphorylate Ser’s side chain.
Why is the intracellular pH so important for protein structure and thus function?
4) Know what atoms make up the peptide bond and how these atoms contribute to secondary structures
(Fig. 3-3a, b, and c). What are the phi and psi bonds?
5) Primary and secondary structures (Figs. 3-4, 3-5, and 3-6),
6) What interactions help fold proteins into tertiary structures (Fig. 2.11 and Fig. 3-7) and quaternary
structures?
7) Protein motifs and domains (Fig. 3-10, 3-11, and 3-12).
8) Homologous proteins: what’s the difference between orthologous proteins vs. paralogous proteins?
9) How do proteins fold properly? (Fig. 3-16).
10) What other proteins or protein complexes help nascent fold proteins, and how do they work (Fig. 3-
17a and 3-18)?
11) What are prions, and what does it mean when we say prion are contagious when misfolded?
12) Know these terms: Ligand, Substrate, Affinity, Specificity, CDR, Antigen, Epitope, Active site,
catalytic site. What actually makes up the catalytic site in a protein enzyme?
13) Enzymes kinetics (basics)
Activation energy, what enzymes do and don't do (Fig. 3-20). Rehash, I know, but it’s important.
Basic definitions of Vmax, Kcat, and Km. The relationship between Km and affinity.
You should be able to recognize the Michaelis-Menton equation and have an idea of what it's
describing.
14) Post-translational modifications: covalent acetylation, phosphorylation, methylation, glycosylation.
- The effect of acetylating Lysine’s side chain.
- What amino acids can be phosphorylated?
- What are kinases? What are phosphatases?
- What amino acids can be methylated? What does methylation do for the side chains?
- What amino acids are glycosylated (e.g., O-linked versus N-linked)?
15) What non-covalent allosteric modifications did we describe?
- What are Guanine nucleotide switch proteins?
16) Extra-cellular proteases and peptidases
17) Intracellular protein degradation
a) Lysosomes
b) The ubiquitin pathway
Ubiquitin, E3 ligases, the proteasome. What happens to ubiquitin at the proteasome?
18) Methods for protein purification
Centrifugation: Differential versus rate-zonal versus equilibrium density (Figs. 3-37 and 4-37).
What are Svedberg units?
Electrophoresis:
Ionic and non-ionic detergents.
What does SDS do to proteins? Does SDS break covalent bonds?
Isoelectric focusing and SDS-PAGE. What the heck does isoelectric mean?
19) Methods for protein purification (continued)
Column chromatography (Fig. 3-40a, b, and c):
a) gel filtration: separation based on___________________
b) ion-exchange: separation based on__________________
c) affinity chromatography: separation based on____________________
Western blotting (Fig. 3-41a and b).
What is it good for?
Radioactive isotopes (Table 3-1)
Which isotope could you use to label DNA? A protein during its
 synthesis in the cytoplasm?
20) What is a Pulse-Chase experiment?
21) Proteomics (aka, “biochemistry” in-the-day)
Edman degradation
Time-of-flight mass spec. MOLDI-TOF (Fig. 3-43)
Electrospray ionization (ES) spectrometry (Fig. 3-44)
In vitro peptide synthesis: what’s unusual about this?
X-ray crystallography. (Fig. 3-45) What’s a synchrotron?
Cryoelectron microscopy making a huge come-back (Fig. 3-46).
Tandem MS/MS and then Liquid Chromatography MS/MS (Fig. 3-47)
NMR spectroscopy

Chapter 4: Culturing and Visualizing cells. We’ll do microscopy first.

1) Difference between magnification and resolution. What factors are important for best resolution?
Maximum resolution for a good light microscope is _________?
2) Types of light microscopy (lecture slides are best).
Diffraction and refraction.
Why do you use immersion oil with the high power lenses?
3) What is fixation and embedding? What machine do you use to section embedded tissues?
4) Antibody labeling of cell components (Indirect Immuno-fluorescence Microscopy)
5) Fundamentals of epi-fluorescence microscopy (Fig. 4-9d, but lecture slide is better).
6) What is the Green Fluorescent Protein and its derivatives, and how can we use them? (Fig. 4-16)
7) Houston, we have a problem: What inherent problem exists in the conventional fluorescence
microscope shown in this figure? (Fig. 4-17)
8) Confocal, deconvolution, two photon, and TIRF microscopy to the rescue!! (Figs. 4-18, 4-19, and 4-20
and 4-21).
9) FRAP (Fig. 4-23)
10) FRET (Fig. 4-24 and 4-25)
11) Super-resolution (Fig. 4-26)

I’m guessing we get this far by the end of lecture 8 on Friday, Jan. 31. But just in case we’re overly-
ambitious:

12) Light-sheet (Fig.4-27)

13) Transmission electron microscopy (TEM) (Fig. 4-28, lecture slides). Why do you use heavy metal salts
like lead citrate and uranium acetate to stain thin sections of cells for TEM? Resolution for TEM is
______. What kind of lenses is used in a transmission electron microscope? What is immuno-electron
microscopy? Why gold? (Fig. 4-33)
14) Cryo-EM/Tomography
15) Scanning EM

Back to culturing cells:

16) FACS (Fig. 4-2). So, can FACS distinguish between G1 cells, versus cells in S phase, versus G2 cells?
17) Making Monoclonal antibodies (Fig. 4-6)
Sample questions. (Question number 6 below doesn’t list the structures, but you get the idea.)

1) The cell theory has four parts to it. Who stated, “All cells come from cells” (“Omnis cellula e
cellula”)?
A) Lodish B) Schleiden C) Schwann D) Virchow E) Watson

2) Which one of the following choices is FALSE? The archaea are important for the study of cell
biology because
A) they diverged from bacteria after bacteria diverged from eukaryotes.
B) they diverged from eukaryotes after eukaryotes diverged from bacteria.
C) they share many similarities of both bacteria and eukaryotes.
D) many of them afford us the chance to see how life survives in harsh environments.

3) Which one of the model organisms best serves to explain the differentiation of the human immune
system?
A) The bacterium, Eschericia coli.
B) The yeast, Saccharomyces cerevisiae.
C) The round worm, Caenorhabditis elegans.
D) The fruit fly, Drosophila melanogaster.
E) The mouse, Mus musculus.

4) Of the macromolecules within the cell, which class is considered to be the most dynamic in structure
and function?
A) Polysaccharides. B) Proteins. C) RNA. D) DNA. E) Lipids.

5) Of the macromolecules within the cell, which class indirectly regulates the synthesis of the others?
A) Polysaccharides. B) Proteins. C) RNA. D) DNA. E) Lipids.

6) The structure drawn on the left is_________; while the one on the right is___________
A) alanine; glycine
B) leucine; lysine
C) serine; cyteine (Know your amino acids!! And the post-translational
D) valine; proline modifications that can be made to them)
E) phenylalanine, tyrosine

7) The most important characteristics in folding a protein into its proper three dimensional structure is
A) hydrogen bonds that form between serine side groups and glutamine side groups.
B) the energetically unfavorable effects between hydrophobic amino acid side groups and their
surrounding aqueous environment.
C) ionic bonds that form between glutamic acid and arginine residues.
D) the addition of ubiquitin to the protein followed by proteosome interaction.
E) disulfide bonds that form between cysteine residues.
8) Which of the following post-translational modifications makes Ser acidic?
A) Phosphorylation
B) Glycosylation
C) Acetylation
D) Methylation
E) Ubiquitylation

9) Which one choice below is TRUE?

A) Enzymes increase the equilibrium constant (Keq) for a reaction.
B) The equilibrium constant (Keq) is the same as the initial forward reaction rate.
C) Equilibrium for a particular step in a series of biosynthetic reactions is the same as steady
state.
D) pH = pKa of a particular weak acid when half of this weak acid (HA) has dissociated into H+
and its cognate base (A-).
E) pH = -log[OH-].

10) Which of the following is used to buffer the cytosol within cells?
A) Hydrochloric acid (HCl).
B) Acetic acid (CH3COOH).
C) Phosphoric Acid (H2PO4-).
D) Formaldehyde (CH2O).
E) Ammonia (NH3).

WARNING: I write new exams every semester. So

it will be a horrific mistake if all you study are old
exams. It’s best to just learn the material.