Biology notes, term 2
1. Identify criteria used to measure complexity.
• The number of cell types can be used as a measure of complexity, directly
analogous to embryonic development where a single celled zygote
becomes a multicellular organism
• Increased compartmentalization of cells and the increased interaction
between them. Increased gene activity
• Increase in organismal size is not a criteria used often because lineages
tend to vary in size increase or decrease. Evolution often leads to a
decrease in size, often for reasons other than to streamline complexity
• Life style is used as a measure of complexity, often in parasites. A parasite
may utilize several different intermediate hosts before reaching its adult
stage and settling down in a single host
2. Identify the main structural components of Chlamydomonas cells.
• Two flagella, mitochondria, an eye spot embedded in a chloroplast, a
nucleus and vacuoles
3. Identify the relationship between Chlamydomonas and the evolutionary common
ancestor of animals and plants.
• Chlamydomonas is somewhat intermediate between animals and plants. It
has a chloroplast and does photosynthesis but it also has the eukaryotic
flagella that was lost in land plants but remained among animals • Unlike land plants, it grows in the dark utilizing an organic carbon source
but retains the ability to do photosynthesis if necessary
• Since Chlamy has more recently diverged from the plant-animal common
ancestor, it retains many eukaryotic features flowering plants have lost
(like flagella and centrioles). This makes it a valuable model organism for
the evolution of eukaryotes
Lecture 1 Lecture
1. Roles of light as used by life
• Information (sight)
• A source of energy (photosynthesis, photolyase)
2. Characteristics of Chlamydomonas that make it a useful model system
• The genome sequence shows animal and plant attributes. It is distantly
related to both and is simple enough to help understand the basic biology
of eukaryotic plants and animal
3. Function of basic components of Chlamydomonas cells
• The nucleus: DNA stuff takes place here (gene expression, transcription, etc.)
• The basal body: found at the base of any cilium or flagellum (where
microtubules develop to produce the flagellum)
• The flagellum is basically identical to that of humans and is used for motility
• The endoplasmic reticulum, ribosomes, cytoprotein synthesis, Golgi: for
packaging and assorting proteins
• Mitochondria (multiple): ATP synthesis, cellular respiration • The chloroplast (one): energy transduction and photosynthesis happens here
• The pyrenoid: where carbon fixation takes place
• The eyespot: found within the chloroplast, enables Chlamy to orient itself in
relation to light (detects the light and translates the information to movement)
4. Relative usefulness of various biological characteristics as measures of complexity
• A complex system requires more than one entity. These multiple entities come
together and if one entity does not function, the system doesn’t function
• One measure of complexity is cell size. Chlamy is a single cell but is very
large, much bigger than a single celled bacterium
• Genome size is not a good measurement of complexity (C value paradox)
• Number of protein coding genes is another measure because most of the
genome is non-coding so this measurement is more useful
5. Advantages to Chlamydomonas in being phototactic.
• Phototaxis: movement towards or away from light
• This allows Chlamy cells to regulate how much light they do or do not
receive, allowing greater control over the photosynthetic pathway
6. Reasons why Chlamydomonas might move AWAY from a light source.
• Too much light may cause photosynthesis to run out of control, leading to
a dangerous buildup of the products of photosynthesis, most notable
reactive oxygen species (free radicals)
7. Basic structure of rods and cones as photoreceptor cells.
• Rods and cones have stacks of disks which are photoreceptors • A cellular membrane on the photoreceptor cell encloses the stacks of
8. Major components involved in phototransduction and their role
• The active pigment in a photoreceptor changes and activates a protein
called transducin, which then activates the enzyme phosphodiesterase
• The sodium pump is bound by cyclic GMP and sodium is transported into
the cell. But phosphodiesterase, the cyclic GMP has a phosphate group
cleaves and the sodium channel is deactivated, generating an action potential
• Light shuts down the sodium pump and the membrane hyperpolarizes
Lecture 2 lecture
1. Relationship between excited states of a pigment and its absorption, fluorescence
• The excited states of a pigment match the absorption spectrum
• Its fluorescence is shifted to a longer wavelength (the emission spectrum)
• Absorption characteristics reflect the excited states
2. Region of the electromagnetic spectrum known as “visible light”.
• A very narrow region of the EM spectrum from 400nm (blue) to 700nm (red)
3. Relationship between wavelength and energy content of a photon.
• The shorter the wavelength, the higher the energy
• Energy is inversely proportional to wavelength.
• Ex. blue light (400nm) has more energy than red light (700nm)
4. Molecular characteristic of visible pigments that make them able to absorb light. • Pigments have a conjugated system: an alternation between a double bond
and a single bond
• A conjugated system results in many non-bonding electrons (pi orbitals)
• These electrons are accessible to light and can absorb it
• Retinal though, actually uses bonding electrons to absorb light
5. Relationship between pigments and associated protein.
• Pigments are bound very specifically to proteins
• If you isolate the proteins, they have colour because the pigments remain
bound to them. But they are bonded non covalently so one has to be
careful if one wants to leave the pigment attached to the protein
6. Four “fates” of the excited state of chlorophyll resulting from absorption of photons.
• An electron absorbs the energy in a photon.
• A blue photon has enough energy to send the electron to the higher excited state
• Very quickly, some energy is lost as heat and the electron decays to the
lower excited state
• A red photon only gets the electron to the lower excited state
• So it doesn’t matter what kind of photon gets absorbed, very quickly both
end up in the lower excited state
• The energy in the electron in the lower excited state can lose the excess
energy in four different ways (four fates)
• One: the electron can lose that energy as heat • Two: the energy can be lost a little as heat, sending the electron to a sub
lower excited state. The remaining energy can be lost as fluorescence
• The fluorescence is a different red, it is darker (longer in wavelength) than
the original red photon because some energy is lost as heat
• Third: work can be done with the energy (photochemistry)
• The pigment uses the energy to change it’s structure
• Fourth: the energy can be transferred to a neighbouring pigment
7. Reason(s) why relative fluorescence is different in isolated chlorophyll vs. intact
cells when exposed to light.
8. What accounts for the fact that chlorophyll is green in colour
• Chlorophyll is green because there is no “green” excited state.
• Chlorophyll is unable to absorb green light and so the photon is reflected,
or transmitted through that pigment
• The reflected green photon reaches our eye because it is reflected and
chlorophyll appears green
9. Quantitative relationship between photons and excited electrons.
• One photon excites exactly one electron
• A photon cannot excite more than one electron, or less than one electron
10. Relationship between energy of photon and energy required to excite electrons in
order for photons to be absorbed. • For the energy to be absorbed, the energy in the photon must match the
energy needed to bring the electron from the ground state to the excited
state. That’s why green photons are not absorbed, the energies don’t match
any of the excited states
11. General structure of photosystem.
• The antenna surrounds the reaction centre. The antenna contains many
pigments that ferry the energy from the photons to the reaction centre
12. Similarities and differences of the light capturing and photochemistry of
phototransduction (retinal) vs. photosynthesis (chlorophyll).
• The photochemistry of phototransduction takes place in the photoreceptor
• It causes the isomerization of the pigment retinal
• In photosynthesis, the light is captured by the photosystem
• The energy is shifted in the antenna from one pigment to another (energy transfer)
• No photochemistry in the antenna, no electron movement
• Photochemistry occurs when the energy reaches the reaction centre and
the electron is pulled off and used to drive electron transport
13. How are excited states of antennae pigments organized to provide for energy
transfer to reaction centre?
• The antennae pigments are placed very close to each other to allow energy
to be transferred from one to another. The distance must be very small
• The energy is transferred through resonance. The absorption and emission
spectrum of the two pigments must overlap • The dipoles of the two pigments must align
14. Structure of rhodopsin.
• Rhodopsin = retinal + opsin
• Retinal is a pigment bound by the protein opsin
15. Effect of photon absorption by 11-cis retinal on retinal structure followed by
association with opsin protein followed by interaction of transducin with opsin.
• When a photon is absorbed by 11-cis retinal, the double bond breaks and
reforms to become all-trans retinal (photoisomerization)
• Absorption of a photon excites the bonding electron and the bond is broken
• Isomerization leads it to detach from opsin (note: no detaching in a
photosystem) and this changes the shape of the opsin
• Transducin can now interact with new shaped opsin and posphodiesterase
is activated and leads to the events required for vision
16. Reasons why life has evolved to detect the narrow band of energy represented by
• Visible light is the most dominant wavelength of light
• Ozone does not allow much UV light to penetrate the atmosphere
• Visible light is energetically perfect. It does not have an extreme amount
of energy (like X-rays and gamma rays do) but it has enough energy to
excite an electron (not like radiowaves and microwaves do)
• To recap: abundant and energetically perfect
Lecture 3 1. Basic structure of an amino acid and what are the different classes of amino acids.
• An amino acid has a central carbon atom bonded to an amine group (NH ) 3
and a carboxyl group (COOH) and a hydrogen atom
• It is also bonded to a variable R group, called a side chain
• The R group varies widely and gives the individual amino acids their
• There are 20 unique amino acids, commonly grouped by the properties of
their side chains
• These groups are nonpolar amino acids, uncharged polar amino acids,
negatively charged (acidic) polar amino acids, and positively charged
(basic) polar amino acids
2. Chemistry of the peptide bond and how it is formed.
• A peptide bond is formed by dehydration synthesis between the NH 3
group of one amino acid and the COOH group of another.
• Because of this, an amino acid chain always has a NH gr3up at one end
(called the N-terminal end) and a COOH group at the other end (called the
C-terminal end). In cells, amino acids are only added to the C-terminal end
• The peptide bond is a covalent bond
3. The four levels of protein structure.
• The primary structure is just the sequence of amino acids in a protein
• The secondary structure is the individual regions of alpha helices, beta
sheets, and random coil in a polypeptide chain • The tertiary structure is the overall three dimensional folding of a
• The quaternary structure is the arrangement of polypeptide chains in a
protein that contains more than one chain (like in hemoglobin)
• Each structural level depends on the one before it
4. What bonding arrangements give rise to primary, secondary and tertiary structure?
• The primary structure is determined simply by its complete amino acid
sequence which is determined by the nucleotide sequence of the protein’s
• The secondary structure is based on the hydrogen bonds between the
atoms of the backbone which form between the hydrogen atom attached to
the nitrogen of the backbone and the oxygen attached to one of the carbon
atoms of the backbone
• The tertiary structure is formed by interactions between R groups. These
are ionic bonds, hydrogen bonds, hydrophobic interactions, and disulfide
bridges. The tertiary structure is somewhat flexible allowing some
conformational changes to protein structure
• The quaternary structure is formed when two or more polypeptides come
together to form a functional protein
5. How are alpha helices and beta sheets formed?
• An alpha helix is formed when hydrogen bonds form between every N-H
group of the backbone and the C=) group of the amino acid residues
earlier in the chain • A beta sheet is formed by side-by-side alignment. The two strands form
hydrogen bonds between them
Lecture 3 lecture
1. Reasons why photosystems have antenna proteins while the eye doesn’t.
2. Points of control for regulation of protein abundance.
• Control of transcription, control of translation, control of transcript
abundance and mRNA decay
3. Factors affecting mRNA transcript abundance.
• mRNA decay competes with the process of transcription
• mRNA decay and transcription both work to determine transcript
abundance (one determines how much is made, the other determines how
much is degraded)
4. Steps in making a Northern Blot for measuring mRNA transcript abundance.
• RNA is isolated from cell or tissue samples
• RNA is run on a gel in gel electrophoresis
• The RNA is transferred onto a nylon membrane
• Since mRNA is a fraction of total RNA (most is rRNA), a radioactive
gene-specific probe that hybridizes to the specific mRNA because the
sequences are identical
• When the mRNA is now exposed to film, the radioactive probe allows a
picture to be produced of the relative abundances of the mRNA
5. Relative abundance of various types of RNA in typical cells.
• 6. Steps in making a Western Blot for measuring protein abundance.
• SDS-PAGE gels are stained and run in an electrophoresis machine
• The gel is transferred to a membrane and probed with an antibody for the
specific protein one is looking for
7. Characteristics of constitutive vs. induced vs. repressed gene expression kinetics.
• Constitutive expression: gene expression does not change
• Induced expression: transcript abundance goes up
• Repressed expression: transcript abundance goes down
8. Varieties of defects that might account for lower levels of functional
• rgIII mutation in mice affect vision
• The functional photoreceptors and photoreceptor cell are much lower than
in wild type mice
• Transcription could be shut down, the mRNA could be decaying too
quickly, a mutation in the transcription factor shuts down gene expression,
there is a mutation to the opsin gene and the gene makes the wrong protein
(it doesn’t fold correctly)
• Retinal biosynthesis is defective. Retinal is NOT coded by a gene. Retinal
is the product of a biosynthetic pathway but the enzymes needed to
catalyze the reaction are coded by genes
• A mutation in one of the enzymes could affect retinal biosynthesis
9. Relationship among polypeptide, apoprotein, cofactor and functional protein. • Retinal is a cofactor needed for the effective functioning of its apoprotein
opsin (this is post-translational modification)
• An apoprotein is a protein before it accepts its cofactor
• An apoprotein and its cofactor make a functional protein
• All protein pigment complexes go through post-translational modification
but not all proteins in general do
10. Relationship between protein folding and function.
• For a protein to be functional, it has to fold and acquire a correct three
dimensional shape (conformation)
• A polypeptide isn’t functional; a protein is a functional protein that has
folded. The three dimensional shape is very exact
• The correct shape is called the native conformation
11. Factors affecting proper protein folding (Anfensen's dogma)
• If you have an enzyme with a correct tertiary shape, you can measure the
product of the reaction it catalyzes (say, the change in colour)
• Anfensen took an enzyme in a test tube, measuring the amount of product
produced by the change in colour. He then added urea, which denatured
the protein by disrupting the bonding arrangements which give rise to the
tertiary structure. Now there is no colour change
• After the urea is removed from the polypeptide, the enzyme refolds into its
native conformation showing that protein folding is spontaneous and occurs
in milliseconds. • Folding is dependent only on the primary sequence of the polypeptide.
Given the same sequence, it will fold in the exact same way
1. Isolated, closed and open systems.