Modified from Carley Karsten, 2013
Lecture 5-7 Study Guide
I have organized some terms and topic that I think are important. This does not mean that
other topics mentioned during lecture or in the book will not be tested. This guide is meant
to clarify and emphasize certain points, NOT to list everything you need to know. I will focus
on tying things together across lectures, and giving real-life examples of the biological
principles that we are learning. Details that I include that I think will be helpful, but that you
don’t need to know, I will write in green. Questions to think about I will write in blue.
CLARIFICATION – Enzymes and receptors are specialized “proteins.” You will often hear me
refer to enzymes and receptors as proteins.
Lecture 5: Endomembrane system
1. Endomembrane system = nuclear envelope + ER + Golgi + lysosomes + vacuoles +
vesicles + plasma membrane. NOT mitochondria, chloroplasts, or peroxisomes. All of
these organelles are enclosed by the same type of membrane. This makes exchange of
materials via vesicle transport very easy.
2. Nucleus
a. contains DNA + chromatin, and nucleolus
b. DNA  RNA takes place in nucleus
c. enclosed by double membrane + nuclear lamina (remember: nuclear lamina is
made from intermediate filaments). This “nuclear envelope” is studded with
pores (nucleoporins) which regulate traffic into and out of the nucleus.
d. nucleolus: synthesis of rRNA (“r” = ribosomal), and assembly of ribosomal
subunits (ribosomes are made mostly of rRNA). Subunits are sent out of the
nucleus, and form MATURE ribosomes in the cytosol.
3. Ribosomes: RNA  protein
a. free: located in cytosol. synthesize cytosolic proteins.
b. bound: located on rER membrane. synthesize integral membrane proteins and
secreted proteins. Hint to remember this: rER sends vesicles to Golgi, then to
plasma membrane. So things made in the rER end up either IN the membrane, or
leaving FROM the membrane.
4. Endoplasmic reticulum (ER)
a. Endoplasmic Reticulum (ER): membrane is continuous with nuclear envelope
i. Smooth ER: metabolic enzymes + Ca2+ stores. No ribosomes.
ii. Rough ER: processing of proteins. folding + glycosylation (addition of
carbohydrates) + transport to Golgi and plasma membrane.
5. Golgi apparatus: finishes, sorts, and ships proteins
transport vesicle
cis face
moves between
trans face
transport vesicle leaves
from rER
of Golgi
cisternae via vesicles
of Golgi
Golgi, bound for membrane
6. Lysosome
a. lysosome membrane fuses with membranes of vacuoles, etc. and lysosomal
enzymes HYDROLYZE macromolecules (Remember: what’s the difference
between dehydration and hydrolysis reactions?)
Modified from Carley Karsten, 2013
b. low internal pH, maintained by proton pump, necessary for lysosomal enzymes to
function (Remember: pump = active transport. This is needed here because the
lysosome is moving H+ against its concentration gradient.)
c. I know I asked this in the last study guide, but it’s important: what are the
differences between lysosomes and peroxisomes?
Lecture 6: Cell Communication
*Note: intracellular means within a cell. intercellular means between cells.
1. Basic process of cell signaling = reception  transduction  response. This generally
occurs by these three basic steps:
a. ligand / signal binds to receptor
b. receptor changes shape or location
c. intracellular cascade begins
2. Signaling Molecules
a. secreted signals: cells release signals into extracellular space
i. paracrine / synaptic = super-short distances
ii. endocrine / hormonal = long distances (e.g. through bloodstream)
b. contact-mediated: cells must be touching
i. gap junctions (in animal cells) and plasmodesmata (plant cells)
ii. cell-surface signals
Question: which types of signals, secreted or contact-mediated, are more likely to
activate intracellular receptors?
3. Membrane-bound receptors
a. G-protein-linked (a.k.a. G-protein-coupled receptors, or GPCRs)
i. ligand binding causes receptor to change shape, allowing G-protein to
bind to it
ii. GTP is hydrolyzed to GDP, releasing energy (in the form of a phosphate
group- more on this in lecture 10!) which is used to start an intracellular
response
b. Tyrosine kinase
i. ligand binding causes receptor subunits to dimerize (two monomers move
together)
ii. ATP is hydrolyzed to ADP, releasing phosphate groups that are used to
cross-phosphorylate both of the receptor subunits
iii. phosphorylated tyrosine kinase regions recruit and activate relay proteins,
which are also phosphorylated (= activated), in order for them to start an
intracellular response
*Tyrosine kinase receptors are often involved in growth. When they aren’t
functioning properly they can lead to cancer. For example, mutations that cause
tyrosine kinase subunits to be phosphorylated ALL THE TIME lead to uncontrolled
growth, since the intracellular pathways leading to growth are ALWAYS ON.
c. Ligand-gated ion channels
i. ligand binding causes receptor to open a channel through which ions pass
ii. VERY IMPORTANT for neurotransmission: we will talk about these a lot
more at the end of the quarter, when we get into neuroscience.
4. Intracellular receptors
Modified from Carley Karsten, 2013
a. receptors located in cytosol or nucleus
b. ligands are typically hydrophobic (can easily cross the plasma membrane and the
nuclear membrane)
Lecture 7: Atoms / molecules / water
1. Emergent property: atoms  molecules  cells  LIFE
2. Strong chemical bonds
a. Covalent: SHARING electrons
i. nonpolar = equal sharing (symmetrical)
ii. polar = unequal sharing (usually involves an electronegative atom such as
oxygen)
b. Ionic: TRANSFER of electrons (you usually end up with a positively-charged atom
and a negatively-charged atom) (e.g. Na+ Cl- = table salt)
3. Weak chemical bonds: generally, just simple attraction between a weak positive charge
and a weak negative charge (e.g. hydrogen bonding between the partially-negative
oxygen of one water molecule and the partially-positive hydrogen of another water
molecule)
*Note: “hydrogen bond” does NOT mean a bond between two hydrogen atoms. It is
always between one hydrogen atom and another type of atom (usually something
electronegative- from the righthand side of the periodic table- such as oxygen or
nitrogen).
Question: draw two water molecules. Identify the covalent bonds (polar or nonpolar?)
and any hydrogen bonds that might be able to form.
4. Water is amazing. Consider its cohesive and solvent properties and all that is possible
because of them. It’s no mystery that water is essential for life.
a. cohesion: due to hydrogen bonds between water molecules. causes surface
tension and capillary movement.
b. solvent: due to hydrogen bonds between water and other molecules. causes
hydration shells, and isolation of fatty acids’ hydrophobic tails.
c. Bottom line: the polarity of water, and the fact that it so easily forms hydrogen
bonds with itself and other molecules, makes it a very useful molecule.
5. Acids and bases: this can get complicated. I will try to focus on the most important parts.
a. whenever you see an equation like this: H2O  H+ + OHremember that the double arrow means that the molecules are constantly
shifting between the lefthand side and the righthand side of the equation.
Whatever you do to the solution may make one side more likely to occur than the
other, but they are always, always, always changing.
b. acids = can donate H+ to a solution
low pH = acidic solution = high concentration of H+ (because there are a lot of
molecules around that are donating H+)
c. bases = can pick up H+ from a solution (often negatively charged, but not always)
high pH = basic solution = low concentration of H+ (because there are a lot of
molecules around that are removing H+)
*Note: H+ does not exist in nature. H+ is shorthand for H3O+, a form of water that
occurs at high pH.
d. acidity and basicity is all relative. A given molecule could potentially act as an acid
Modified from Carley Karsten, 2013
OR a base, depending on the pH of the solution you put it in. When trying to figure
out if something is an acid or a base, ask yourself if it is more likely to give up a
hydrogen or to gain a hydrogen (see below).
6. Buffers: weak acid / weak base pair that helps to maintain constant pH in biological
systems by accepting and donating H+ as needed.
Bicarbonate buffering system (VERY important for maintaining constant blood pH):
H2CO3  HCO3- + H+
In this system, and any other buffer problem you might be asked, a few notes…
-- the H+ on the right is ONLY there to balance the equation. It does NOT indicate acidity. Just
ignore it.
-- H2CO3 is the weak acid. Why acid? Because it has more hydrogens to give away.
-- HCO3- is the weak base. Why base? Because it can pick up another hydrogen.
-- IF H2CO3 gives away a hydrogen, notice that it BECOMES HCO3-. Also, if HCO3- picks up a
hydrogen, it becomes H2CO3.
-- If you add a strong acid to this system, which product will you end up with more of? What
if you add a strong base? To help figure this out, draw diagrams!! Which molecule will pick
up excess H+ after you add the acid? What will that molecule look like after it has picked up
the extra H+?