Below is an organized, brief summary of the concepts and content
that
our lectures have covered.
It is to be used as a guide to direct your study, not as a substitute
for your notes or the sections of the text that fully describe these
concepts.
I. Chemistry
A. Bonds
1. covalent:
equal sharing of two electrons between atoms
2. ionic:
one or two electrons donated to another atom. Forms + and - charged
ions
in
water
3. polar
covalent: electrons not shared equally. One atom is more electronegative.
Causes dipoles (slight + or - sides) in the molecule.
4. hydrogen:
polar molecules attracted to other polar molecules through oppositely
charged
dipoles.
B. The water molecule
1.
structure
2. types
of hydrogen bonds it makes
3.
interactions
with ions
4. hydrophilic
molecules dissolve in water (are polar or charged). hydrophobic
do not
(non-polar)
C. Principles of organic chemistry
1. based
on carbon
2. built
around a carbon skeleton
3.
modified
by addition of functional groups
4. may
form isomers: Molecule has same chemical formula but
not
the same exactly
a. structural: different bonding
relationships
b. stereoisomers:
same bonding relationships but
orientation
is different around a
double-bond
(cis on same side; trans on opposite sides)
c. enantiomers:
mirror image molecules. Exist in L (left-handed) or D (right-handed)
forms. A special form of stereoisomer.
5. polymers
formed by condensation (dehydration) reactions (Removal of one
OH
and
one H from two monomers to form a water molecule. Everything left is
covalently
linked.)The opposite is
hydrolysis, where the newly formed bond would be broken,
releasing
energy. This requires the addition of
water.
II. Biological Molecules
A. proteins
(polypeptides)
1. polymer of amino acids
2. formed by condensation synthesis between the carboxyl
group of one amino
acid and the amino group of another amino acid. Forms peptide
bonds
3. amino acids are the monomer
a. centrally located carbon bonded to a H, a carboxyl
group, and an amino group in all
amino acids
b. specific amino acid is determined by the R
group
or side chain attached to
the central carbon
c. L enantiomeric forms are active, D are not
d. classified as nonpolar, polar, acidic, or basic
depending on the side chain. 3 do not easily classify.
4. First amino acid in the polypeptide has an intact
amino group (amino terminal) and
last amino acid has an intact carboxyl terminal (carboxy terminal)
5. Four orders of protein structure
a. Primary structure: amino
acid sequence of the polypeptide
b. Secondary structure:
Path
of the polypeptide backbone stabilized by
hydrogen bonds between the peptide linkages. alpha helix or beta-pleated
sheet
most common.
c. Tertiary structure:
Three
dimensional shape of a polypeptide. Stabilized by
hydrogen bonds, ionic bonds, hydrophobic interactions (caused
by
non-polar side chains trying to get away from water), and van der
Waal's
forces, predominantly between the side chains.(caused by
electrons
moving in their
orbitals around the atoms, transiently attracting or repelling the
atoms.)
Disulfide
bridges sometimes form between two cysteines. (The cysteine SH
(sulfhydryl
group)
reacts with the same on the second cysteine, forming a S-S
covalent
linkage.)
d. Quaternary structure:
More
than one polypeptide interacting in order for a
protein to function. Example: hemoglobin.
-some proteins require a prosthetic group also to function.
(example: heme in hemoglobin)
B. Polysaccharides
1.
Monomer is the monosaccharide.
(sugar)
2.
CH2O is the general formula. Contains a ==O
attached to one of the carbons.
3. If 5 or 6 carbons, will spontaneously form
ring structures.
4. If
C1 has its OH below the plane of the ring, it is called an alpha form,
if above it is called a beta form.
5. Glycosidic
linkage is formed form a condensation reaction occurs between two
monosaccharides. The first loses an OH and the second a H.
6.
Polysacchardie that forms from all beta glucose monomers is called cellulose.
a. rigid, inflexible structure.
b. used to make plant cell walls
7.
Polysaccharide that forms from all alpha glucose monomers is either
called starch, in plant cells,
or glycogen in animal cells.
a. both are storage forms of energy used for
quick energy needs. Starch is less branched than glycogen.
C. Lipids
1. triglycerides
a.
formed when one glycerol molecule reacts in 3 condensation reactions
with 3 different fatty acids.
b. bonds formed are ester bonds.
c. fats are white, solids in animals; oils are yellow
liquids in plants.
d. used for long term energy storage.
2. phospholipids
a. glycerol-derivative used has two condensation reactions
with two fatty acids.
b. the third carbon is attached to a phosphate. That can be
attached to something else in a specific phospholipid.
c. amphipathic chemical behavior due to hydrophobic fatty
acid tails and hydrophilic phosphate group region.
d. perfect structure for cell membranes
3. steroids
a. fused rings and hydrocarbon, primarily hydrophobic, with
a small polar group (OH usually) attached to part of the rings.
b. cholesterol is an example, part of cell membranes.
c. some are hormones like estrogen or testosterone.
III. Cells
A. Small
size maximizes surface area to volume ratio.
B. Two
major categories of cells are prokaryotic (bacteria) and eukaryotic
(fungi, plants,
and animals)
C.
Eukaryotic
cells have internal membranes and membrane-bound structures,
prokaryotic
cells do not.
D.
Eukaryotic
cells are classified as plant cells or animal cells
E.
Eukaryotic
structures we discussed include:
1. nucleus: contains the
DNA
a. ribosomal RNA genes are located in the nucleolus
b. surrounded by a nuclear envelope consisting of
inner
and outer membranes
interspersed with nuclear pores through which molecules travel into and
out of
the nucleus.
2. ribosomes (also found in prokaryotes)
a. synthesize the proteins for the cell
b. can be free floating in the cytoplasm
c. can be attached to the endoplasmic reticulum
d. consist of rRNA and rproteins
3. endoplasmic reticulum
a. rough ER has ribosomes attached tha make
proteins
destined for either secretion,
the cell membrane, or a lysosome or plant vacuole or a secretory
vesicle.
b. smooth ER has no ribosomes. Synthesizes
lipids
such as steroids and
phospholipids. Detoxifies drugs, e.g. alcohol.
c. consists of a series of elongated membrane bound
sacs.
Internal region
is fluid filled, called a cisternal space or lumen
4. Golgi apparatus
a. pancake-like membrane bound sacs
b. molecules transported from ER in transport
vesicles
enter it at its cis face
c. different modifications made to the molecules as
they
move from sac to sac
d. molecule moves out the trans face
in a transport vesicle to its final location
5. Lysosome
a. hydrolytic enzymes transported there from
the
trans-Golgi
b. is a membrane bound vesicle that degrades larger
molecules
and structures
6. Mitochondria
: will cover later. Not on first exam.
a. site of most ATP production in eukaryotic cells
7. Chloroplast: will cover later. Not on
first exam.
a. site of photosynthesis. Only in plant cells.
8. Cytoskeleton:
a. polymers of proteins that criss-cross eukaryotic
cells
and contribute to cell
movement, communication, and attachment, etc.
b. microfilaments: polymers
of actin
c. microtubules:
polymers of tubulin
d. intermediate filaments: not
well defined
V. Cell Membrane
A. All
cells must have a cell membrane
B.
Membrane structure
1. mainly phospholipd bylayer oriented with
polar
heads outward and inward interacting
with water and the hydrophobic tails inside, interacting with each
other.
a. Phospholipids are an example of a biological
molecule
in the lipid family.
b. Consist of a hydrophobic region (two fatty acid
tails) and a hydrophilic region (the
phosphate and its modification.
c. In water, phospholipids form bilayers with the
fatty
acid tails interacting with each
other and the phosphate head regions orientented to either side,
interacting
with
water.
2. Double bond (unsaturated) in the
hydrophobic
tail causes a kink that prevents the
phospholipids from entangling. Helps keep membrane fluid.
3. Cholesterol, another member of the lipid
family,
is interspersed between
the phospholipids and also helps keep the membrane fluid.
C. The
Extracellular
Matrix
1. Secreted by cells and containg protein,
polysaccharide,
etc. The composition is
variable.
2. Serves various roles, such as adherance,
connective
tissue structure, bone deposition
etc.
D.
Cytoskeleton
1. Microfilaments often connect to membrane proteins
allowing communication between
the membrane and the internal region of the cell.
Smallest diameter. Made of actin
2. intermediate filaments are ropelike and criss-cross the
interior of the cell.
3. microtubules are the widest. Form structures like the
spindle that forms during cell division.
VI. Simple Diffusion
A.
Movement
of molecules across a membrane that is permeable to them
1. Net direction of movement is from the more
concentrated
side to the less concentrated
side
2. This will continue until the concentration is
equal
on both sides
a. Called equilibrium
B. If
more than one type of molecule is present and the membrane is permeable
to both,
they move independently of one another, following their own
concentration
gradients.
C. Energy
comes from favorable entropy changes as the system moves towards
equilibrium. (potential energy stored in the concentration gradient).
VII. Osmosis
A. The
diffusion of water molecules across the cell membrane
B.
Determined
by the water concentration (moves higher to lower)
C. This
is determined by the total solute concentration of solutes
that
cannot cross the
membrane.
1. Water moves from region of lower solute conc. to
region
of higher solute conc.
D. Region
with higher dissolved solute conc. is the hypertonic solution,
compared
to the
region of lower dissolved solute conc. which is the hypotonic
solution.
E. Water
moves from the hypotonic side to the hypertonic side
F. If
solute concentrations are equal, the two solutions are isotonic and
there is no net
water movement
G. In
animal cells, to be in isotonic solution is best, hypertonic causes
cells
to shrivel,
hypotonic causes cells to burst.
H. In
plant cells, to be in hypotonic solution is best (causes turgor),
isotonic is all right but
cells are not as firm as in hypotonic, and hypertonic causes
plasmolysis.
VIII. Passive Transport
A. Does
not require additional energy besides that provided by the
concentration
gradient of
the transported molecule
B. Net
movement of the molecule is with the concentration gradient.
C. Three
types
1. Simple Diffusion (Described above)
2. Osmosis (Described above)
3. Facilitated Diffusion
a. molecule is not free to diffuse directly through
the
membrane
-either has a charge, or is too large
b. uses the assistance of a membrane protein, called
a carrier.
c. transport protein binds specifically to the
molecule
to be transported
-causes the transport protein to change shape and the molecule is
deposited
on the
other side of the membrane.
-net movement is with the concentration gradient
d. also occurs using channel proteins, some gated, some
not. Aquaporin is an ungated water channel. Molecule is shielded from
the hydrophobic
bilayer and can therefore diffuse across the membrane.
IX. Active Transport
A.
Movement
of a molecule across the cell membrane against the concentration
gradient
B.
Requires
energy
1. ATP used in primary active transport
a. Terminal phosphate removed and transfered to an
amino
acid in the transport protein
b. Negative charge on phosphate causes protein to
change
its shape, transporting
the molecule
c. ATP hydrolysis is exergonic, releases energy.
d. This is coupled to the endergonic reaction,
attachment
of the phosphate to the transport protein.
e. ATP can also be used for energy by breaking the
alpha-beta
phosphate bond, releasing PP
(pyrophosphate) which breaks down to 2P. Both reactions release energy.
This mechanism
is not the one used for active transport however.
C. Na+
- K+ pump
is an example.
1. Binds 3 Na+ inside cell
2. Phosphate removed from ATP and transfered to pump
3. Pump changes shape, releasing Na+ outside cell
4. 2 K+ now bind
5. Phosphate removed from pump
6. Pump returns to original shape, releasing K+
inside
cell.\
7. Example of an antiport. (two substances cross membrane
in
opposite directions).
D. Intestinal
Epithelial Cell
1. Uses co-transport to bring glucose from
the
gut into the cell against its conc.gradient
a. energy provided by the concentration of the
cotransported
molecule moving with a
favorable conc. gradient, in this case it is Na+
2. Glucose and Na+ both bind to the Na+ - glucose
symport (example of a symport, moving two
substances across the membrane in opposite directions).
This is secondary active transport.
3. Both are transported together into the cell, using
the energy of Na+ conc. gradient.
4. Na+ - K+ pump operates to remove the Na+ back out
again to maintain the conc.
gradient so the pump can continue to function.
5. Glucose moves out of the cell into the blood by
facilitated
diffusion.
6. Tight junctions maintain these proteins in
their proper location.
E. Exocytosis/Endocytosis
1. Membrane bound vesicles fuse with another membrane such
as the plasma membrane and release contents. (exocytosis_
2. Membrane engulfs the cargo and brings it inside that
way. (endocytosis)
a. When the cargo is another organism or
nutrient it or cell, it is called phagocytosis.
b. When the cargo is liquid, it is called
pinocytosis.
c. When a membrane bound receptor interacts
with the cargo molecule and it travels to the invaginated membrane and
is then engulfed and
enters the cell that way, it is called receptor-mediated endocytosis.
NOTE: In 2010 exam one ends here.
IX. Energy and Enzymes
A. Free
Energy, G, is the energy in a system that can do work.
1. G = H - T delta S
a. H is enthalpy, total energy in the system
b. S is entropy, measure of the disorder of
the
system
B. delta
G = G(final state, products) - G(initial state, reactants)
C. exergonic,
spontaneous reactions have negative delta G
D. endergonic,
non-spontaneous reactions have positive delta G
E. activation
energy is energy needed for the reactants to reach the
transition
state
1. The activation energy value does not change the
delta
G of the reaction
2. The transition state is the disordered and
strained
bonding relationships of the
original reactant or reactants needed to allow for new bonds to form.
F. Catalysts
are other molecules (not reactants) that interact chemically
with
the reactants
and lower the activation energy of the reaction. At the conclusion of
the
reaction they are
unchanged.
G. Enzymes
are biological catalysts
H. Enzymes
lower the activation energy of a cellular reaction by
1. increasing local concentration of reactants
2. orienting reactants accurately
3. inducing strain and distortion into the reactants'
bonds
I. Enzymes
bind specifically to their substrates (the reactants) at the
active
site of the
enzyme
J. Enzymes
slightly change their active site's shape as they bind the substrate to
make a
tighter fit. The tightest fit is to the transition state. This is
called
induced
fit.
K. Enzymes
catalyze the reaction after the substrate binds, forming the products
which
cannot fit the active site and are released.
L. Enzymes
are regulated by
1. competitive inhibition.
a. inhibitor has similar shape to substrate
and
binds the active site.
2. non-competitive inhibition
a. inhibitor binds to site on the enzyme away from
the
active site but this causes a
change in the shape of the active site that makes the substrate
bindingt
less
efficient.
3. allosteric regulation
a. these enzymes have quarternary structure
b. they exist in an active or inactive form and can
flip
back and forth
c. an activator will bind to an allosteric
site
(not the active site)on the active form
and stabilize it, preventing it from flipping to inactive. This
increases
the numbers of
active molecules and upregulates the reaction.
d. an inhibitor will bind to an allosteric
site
on the inactive form and stabilize it,
preventing it from flipping to active. This increases the numbers
of inactive
molecules and downregulates the reaction.
e. Metabolic pathways frequently are
regulated
by allosteric enzymes found near the
beginning of the pathway.
f. Feedback inhibition refers to the
end-product
of a metabolic pathway feeding
back and being the allosteric inhibitor of the allosteric enzyme
regulating
the
pathway that produces it.