Session 1

Describe the resolution of the various

microscopes we discussed in class.

To study cell’s key components in atomic

detail –need x-ray crystallography or
cryoelectronmicroscopy

How can the resolution be improved when

using a light microscope (hint: use of dyes,
fluorescent probes, GFP (green fluorescent
protein)).

If you would like to view ribosomes (20nm Transmission electron microscopes

resolution), which microscopes would you
utilize?
If you wish to view your specimen at the
atomic level (<2nm resolution), which
microscopes would you utilize?
Describe the “Cell Theory”. Name the
scientists who defined this theory.
Cryoelectronic microscopy, X-ray
Crystallography
all plant and animal tissues are
composed of cells, and within an
individual organism all the cells are
identical.

Cells are universal building blocks of all living

tissues
Define living cells. Do different animal cell
types have divergent chemistry and genetic
code?
Describe some cellular processes in which
proteins are involved in cells.
All the following statements regarding cells
are CORRECT, except for:
Session 2
All the following statements are TRUE
regarding eukaryotes and prokaryotes
except for:
With respect to Bacteria and Archaea:
a) do they originate from a common
ancestor?
b) do they have different cell wall/cell
membrane characteristics?
c) what is different about the living
environments?
Describe an example of antibiotic
resistance in microbes (e.g., MRSA) and
how this may be a consequence of
evolution.
all LIVING THINGS that are fundamentally
similar inside!
DNA Replication
Transcription
Translation
Metabolic Reactions
Proteins are NOT involved in the replication,
transcription, and translation processes of
the cell. They are ONLY involved in regulating
metabolic reactions that generate the basic
buildings blocks needed for these processes.
Prokaryotes contain endoplasmic
reticulum.
a. According to the evidence, all three
domains of life share a common
ancestor that probably existed
more than 3 billion years ago
b. The composition of the cell wall
differs significantly between the
domains Bacteria and Archaea.
Bacterial cell walls are composed
of peptidoglycan, a complex of
protein and sugars, while archaeal
cell walls are composed of
polysaccharides (sugars).
c. Most archaea are extremophiles
and are found in extreme
environments like the deep sea,
mountains, hot springs, salt brine,
etc. Bacteria reside in different
habitats ranging from soil, water
to inside living, and non-living
organisms.
True
Examples of bacteria that are resistant to
antibiotics include methicillin-resistant
Staphylococcus aureus (MRSA),
penicillin-resistant Enterococcus, and
The development of MRSA is an example of
evolution, specifically in terms of acquired
antibiotic resistance.
What are the four subcellular organelles
in our cells that contain double
membranes?
Describe “endosymbiosis” with reference
to the acquisition of mitochondria and
chloroplasts.
Describe the roles and features of the
following in your cells: nucleus,
endoplasmic reticulum, golgi apparatus
(cis, medial, trans), lysosome,
multidrug-resistant Mycobacterium
tuberculosis (MDR-TB), which is resistant
to two tuberculosis drugs, isoniazid and
rifampicin.
Mitochondria, Golgi Aparatus, Nucleus,
Reticulum Endoplasmic, Chloroplast
Mitocondria : Contain their own DNA
➢Reproduce by dividing
➢Thought to come from bacteria engulfed
by ancestor of today’s eukaryotic cells
➢Symbiotic relationship ensued
Chloroplast:
➢Contain their own DNA➢Reproduce by
dividing into 2
➢Evolved from photosynthetic bacteria
→engulfed by early eukaryotic cell
Nucleus:
Contains the DNA –Genetic Information
peroxisome, mitochondria,
autophagosomes, endosome, plasma
membrane
Mitochondria:
➢Mitochondria have a distinctive internal
structure: Electron Micrograph➢Inner
membrane contains most proteins
responsible for energy production
➢Use energy from oxidation of food
molecules (i.e. sugars) to produce ATP
(fuel to power cellular activity)
➢Consumes O2and releases CO2
(cellular respiration)
➢Contain their own DNA
➢Reproduce by dividing
Golgi Aparatus :
Involved in modifying and packaging
molecules made in ER
➢Molecules transported through golgican
be secreted or transported to another
compartment
Endoplasmic Reticulum →
➢Looks like a maze
➢Site where majority of membrane
components & exported materials are
made
➢Extensive network in secretory type cells
Lysosome
Small, irregularly shape
➢Intracelulardigestion occurs
➢Acidic pH
➢“Bag of enzymes”
Peroxiosome
Sequestered environment for reactions
where H2O2 used to inactivate toxic
molecules
Autophagosomes
double-membraned vesicles that
contain cellular material slated to be
degraded by autophagy
Endosome
primarily intracellular sorting
organelles. They regulate trafficking of

What is the difference between
endocytosis and exocytosis?
In secretory type cells (e.g., melanocytes
and pancreatic beta cells), describe how
melanin and insulin get secreted from
these cells. Are these secretory types of
cells characterized by an extensive
endoplasmic reticulum (and why, if so)?
Describe the cytoskeletal network: actin,
intermediate filaments, microtubules.
- What are the cellular roles of the
cytoskeleton?
proteins and lipids among other
subcellular compartments of the secretory
and endocytic pathway, specifically the
plasma membrane Golgi, trans-Golgi
network (TGN), and vacuoles/lysosomes.
Plasma Membrane
separates the interior of the cell from the
outside environment. ... The plasma
membrane consists of a lipid bilayer that is
semipermeable. The plasma membrane
regulates the transport of materials
entering and exiting the cell.
Endocytosis is the process of capturing a
substance or particle from outside the cell
by engulfing it with the cell membrane, and
bringing it into the cell. Exocytosis
describes the process of vesicles fusing
with the plasma membrane and releasing
their contents to the outside of the cell.
Actin Filaments (A) : determines cell
shape
Microtubules (B) : Microtubules help
segregate chromosomes in a dividing
animal cell
** TEM = Transmission electron
micrograph
** Chromosomes are attached to
microtubules of mitotic spindle
Intermediate Filaments (C) : Intermediate
filaments provide structural support,

Session 3
1. How many neutrons, electrons,
and protons exist in a Hydrogen
atom?
2. How many neutrons, electrons,
and protons exist in a Carbon
atom?
3. What is the atomic mass and
atomic weight of H, C?
- How many grams of carbon will contain
6 X 1023 atoms?
- How many grams of hydrogen will
contain 6 X 1023 atoms?
- How many electrons are there in the
outermost electron shell of H, C, N, O?
- What is stronger: covalent, ionic, or
hydrogen bonds?
- In a water molecule, is the oxygen atom
more electronegative than the H atom?
1. Nucleotides
2. Amino acids (basic structure –
alpha carbon, amino group, R
group, carboxylic group) – are
amino acids linked randomly?
What is the dry mass (in %) of
proteins in cells
regulate key signaling pathways, and
facilitate the movement of proteins to
specific domains of polarized cells, such
as Sertoli cells
1.Mechanical strength
2.Controls its shape
3.Drives/guides its movements
-1,1,0
-6,6,6
C:
Mass : 12,0107 u
Weight: 12
H:
M: 1,00784 u
W: 1
-1,4,5,6
- covalent bonds are the strongest,
followed by ionic, hydrogen bond, Dipole-
Dipole Interactions and Van der Waals
forces (Dispersion Forces).
-Yes, Electronegativity is the attraction of
an atom for the electrons of a covalent
bond. Because oxygen is more
electronegative than hydrogen, the
oxygen atom in water pulls electrons
toward itself, resulting in a partial negative
charge on the oxygen atom and partial
positive charges on the hydrogen atoms.
Nucleotides:
➢ Nitrogen-containing ring compound
(BASE) linked to 5-carbon SUGAR with a
phosphate group
➢ Sugar → ribose OR deoxyribose
➢ Nucleotides with ribose =
ribonucleotides
 3. Monosaccharides
*** please know the bond type (glycosidic
bond, peptide bond, phosphoanhydride
bond, phosphodiester bond, etc) that links
the individual subunits together
*** please know the name of the
macromolecule (protein, DNA, RNA,
disaccharide/oligosaccharide/etc) that is
produced when the subunits are linked
together
*** please know the type of reaction that
occurs to link the subunits together
*** please knnow whether structural
polarity is relevant to the macromolecule
generated
➢ Nucleotides with deoxyribose =
deoxyribonucleotides
C (cytosine), T (thymine), U (Uracil) =
pyrimidines (6-membered ring)
G (guanine) and A (adenine) = purines (5-
membered ring)
BASE + SUGAR = nucleoside
Protein
➢ Carboxylic acid group - Amino group -
Both attached to central α-carbon -
carbon carries specific side chain
Cells use amino acids to build proteins
➢Proteins fold into 3D structure unique to
each type
➢Covalent bond between two amino acids
–peptide bond (formed via condensation
reaction)
➢Resulting chain = polypeptide
Carbohydrate
➢ Monosaccharides – (CH2O)n -
glucose = C6H12O6 ➢ Carbohydrates
➢ Switching orientation of specific OH
groups – can convert it to mannose or
galactose ➢ Two forms: D-form/ L-form
➢ Isomers & optical isomers
➢Monosaccharides can be linked via
glycosidicbonds to form large
carbohydrates
➢Disaccharides (2 subunits)
➢Oligosaccharides (2-10 subunits)
➢Polysaccharides (100-1000s subunits)
➢Condensation reaction (water molecule
expelled) to form bond
➢Break bond by reverse reaction =
hydrolysis (water molecule is consumed)
Lipid

Describe characteristics of fatty acids and
phospholipid molecules. What does the
term “amphipathic” mean? Know the
hydrophilic and hydrophobic components
of a lipid and how this drives the
organization of membrane structure. How
can the membrane lipid fluidity be
altered?
Nucleotides (DNA & RNA):
Phosphodiester
Amino acids (Polypeptide chain): Peptide
Monosaccharides (Glucose): Glycosidic
Phospholipids consist of a glycerol molecule,
two fatty acids, and a phosphate group that
is modified by an alcohol. The phosphate
group is the negatively charged polar head,
which is hydrophilic. The fatty acid chains are
the uncharged, nonpolar tails, which are
hydrophobic
Phospholipids are amphipathic molecules. This
means that they have a hydrophilic, polar
phosphate head and two hydrophobic fatty
acid tails. These components of the
phospholipids cause them to orientate
themselves, so the phosphate head can
interact with water and the fatty acid tails
can't, hence forming a bilayer.
Describe similarities and differences
between DNA and RNA molecules
- What are the bases?
- What are the sugars?
- What is their overall structure (double or
single-stranded)?
- Do they have structural polarity?

The polarity in DNA and RNA is derived

from the oxygen and nitrogen atoms in the
backbone
What is the structure of ATP in terms of
the number of phosphate groups (what
type of bonds links the phosphate
groups?), base, and sugar?

phosphodiester
bond/phosphoanhydride
Session 4

1.
1. Know your amino acids (full name,
three letter code, and one letter
code) if you are given the protein
sequence, be able to identify the
number of non-polar, uncharged
polar, positively charged, and
negatively charged amino acids
2. which amino acids are involved in
mediating disulfide bonds?
3. What is the enzyme that is
involved in producing disulfide 2. Cysteine
bonds in cells? 3. thiol-disulphide oxidoreductases
4. Know which amino acids can 4. serine, threonine, tyrosine
acquire phosphate groups (there 5. Isoleucine, leucine, Lysine
are 3 you must know) – if you are
given a protein sequence, be able
to recognize them.
5. Know which amino acids can
acquire acetyl groups or ubiquitin
modifications
What is the purpose of Chaperones? Do
they require the energy from ATP for their
cellular function?

In which subcellular compartments do The small protein insulin has two polypeptide
you find proteins containing disulfide chains connected by two interchain disulfide
bonds? bonds. There is also one intrachain disulfide.
Cysteine

*Two cysteine side chains can be involved in

the formation of a disulfide bond. Disulfide
bonds help stabilize a favored protein
conformation.

If you have a transmembrane protein an α-Helical Conformation

(spanning the lipid bilayer), where in the
protein structure do you expect to find
mostly non-polar amino acids?
What is a protein family? Do members in
a protein family have similar 3D
structures? Do the members have
different functions?

A protein family is a group of proteins that

share a common evolutionary origin,
reflected by their related functions and
similarities in sequence or structure.
specific functional information that we
can infer.
What is the CAP protein and describe its
structure?
What are the different types of protein
secondary structures (e.g.,. alpha helix,
beta sheets)

What are the different ways of

representing protein structure (e.g.,
ribbon structure, etc)

Describe the antibody structure (IgG).

- Know how many chains comprise its
structure
- Are there disulfide bonds in its structure
– if so, are they intrachain, interchain, or
both?
- Do antibodies have secondary structure
(what type)?
- What are the important regions of an
antibody molecule (e.g., constant,
variable regions)
- How are antibodies generated?
- Can you use antibodies in the laboratory
to conduct experiments?
Be able to match functional classes of
enzymes to their function (e.g.,
hydrolases, kinases, ligases)

What are some examples of drugs that cimetidine, erythromycin, ciprofloxacin,

inhibit enzymes (e.g., HMG-CoA and isoniazid.
Reductase, Dihydrofolate reductase)?
 HMG-CoA reductase (HMGR), a highly
conserved, membrane-bound enzyme,
catalyzes a rate-limiting step in sterol
and isoprenoid biosynthesis and is the
primary target of hypocholesterolemic drug
therapy.
Methotrexate and pralatrexate are
dihydrofolate reductase inhibitors that
deplete cellular tetrahydrofolate cofactors.
How is the activity of Aspartate
Transcarbamoylase regulated – is this an
example of allosteric modulation?

In the laboratory, can you purify native

proteins from cells? Is this laborious? Can
you genetically engineer/produce proteins
and is this easier to do? What method
would you utilize to analyze fractions from
a protein purification procedure?