BIO 4120 Lecture Notes - Glycogen Phosphorylase, Gene Duplication, Tyrosine Kinase

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Published on 12 Apr 2013
School
University of Ottawa
Department
Biology
Course
BIO 4120
Professor
Lecture 1:
- Looking at a comparison between an animal that lives in low temperature
and an animal that lives in high temperatures. Low temp would have a low
rate function, and high temp would have a high rate function. (so graph
would be a straight line). The reason for that is kinetics, kinetics are
temperature sensitive. You can make an animal live at a different
temperature, and its rate function would just shift down the graph. If you
look at rate function (lets say metabolic rate) of goldfish at 25 degrees, and
look at the one that’s adapted to 10 degrees, and if you look at the Antarctic
fish (-1.86 degrees water), they all follow the horizontal line which means
organisms can adjust their metabolic rate within a wide range of
temperatures so basically its always the same. This is called rate
compensation. They have an ability to adjust; they can do that do that on a
seasonal basis, and an on evolutionary basis. Paper that Hochachka/Somero
wrote in 1968 called Adaptation of Enzymes to Temperature and proposed a
mechanism to explain this. They suggested that temperature (besides having
kinetic effect) also could modify activities, meaning it would directly modify
the enzyme and therefore the activity.
- Hard to define adaptation, because its overused and it occurs at all biological
levels. Have an idea of what adaptation is (exam). First definition: basically
increasing fitness in a certain environment. Second: there are certain things
that are important for an organism in the environment and if they don’t
respond to them they die.
- Key ideas are listed in slides. But there are problems with these definitions.
What is an environment? Where the organism lives or the ecological niche
which is controlled by biotic and abiotic factors. Adaptation has to be
considered as optimization process (can solve problems but only to a certain
extent) and there is no such thing as perfection. It is a continuous process
because the environment is constantly changing. If there is a change in the
amount of oxygen, for example a reduced amount in water, the fish increases
amount of water flow across its gills or it could start using anaerobic
metabolism. (different solution for same problem). 3 determinants to
adaptation: first is genome specified which means the genome of that
organism really determines the limits of its adaptational ability (certain
things organisms can do that others cant because they don’t have those
genes). The second thins is its environmentally induced, so environment is
responsible for bringing adaptation to surface. Developmentally defined
means that in certain stages of development you are more likely to adapt.
- Two components of natural selection. One of them is that organisms very and
the variation is inherited in part by offspring. The second component is that
organisms can produce more offspring than can possible survive (Atlantic
cod, produce millions of eggs but only 1 may survive).
- Differential survival is an accumulation of positive or favorable mutations
and those are the ones that will contribute to next generation. Time is
extremely important because evolution doesn’t happen quickly.
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- Must be variability in the organisms like phenotypic plasticity. Evolution
doesn’t start from zero, it relies on variation from the past generation.
Processes are random, thus different phenotypes are possible. No such thing
as the most advanced organisms, but some can be more highly evolved.
Selection is to existing environments, not one that happened before or will
happen.
- --
- Central dogma- protein<-MRNA<-DNA (translation-transcription). Proteins
can be either structural or functional. The protein represents the phenotype
(what organism is going to look like) and DNA represents the genotype. It
suggested that this process always went from DNA to protein; there were
very little issues that happened in between those steps. There have been
many changes since it came out. It was thought that DNA was a blueprint.
DNA is now looked as a recipe (only 1.5% of DNA codes for protein). 65%-
95% of what’s left is actually transcribed but not to protein. We now know it
isn’t unidirectional (reverse transcriptase). Transcription factors are
important in translation (how fast it occurs and which part of a sequence
should be translated). Alternative splicing is removal of certain parts of genes
or editing of them. Post-translational modification is very important because
it changes the complete function of the protein. Can we rely on central
dogma? Yes, protein is still phenotype, and is there at the time that we look at
it.
- All organisms face the same two challenges. Our biochemistry is marginally
stable but physical/chemical factors can modify that stability and if it does it
too much, the protein/function may disappear. How does the organism
compensate for environmental changes?
- Current beneficial trait- if a trait is beneficial to an organism a physiologist
would say that that trait is an adaptation. Exaptation- exploitation of a trait
for an entirely new function. A good example is glycerol, now it is the
“backbone” or a triglyceride. Now they also have another role, used as an
antifreeze. Aptation- beneficial value of trait in absence of historical
understanding (less worried about historical role but if its currently and
important trait).
- Unity is “core program”, as in cells, genes, transcription etc. Divergence is in
the way the genes are expressed. Reason why divergence can be because of
genes sensing changes in environments and transducing signals to
intracellular targets. The non-protein coating genes ( not the 1.5%) are also a
reason for divergence.
Lecture 2
- Cells make energy either by ATP production or ion gradients. If energy cant
be provided under those conditions the animal cant survive. Reducing
equivalents= NADH, NADPH, it is something that has the ability to reduce
some sort of chemical. NADH is important in the electron transport chain.
NADPH is important for biosynthetic processes. (fundamental processes in
all organisms slide)
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- Each of these can be modified by environmental change and can be a focus of
animal adaptation. What kinds of mechanisms can organisms use to ensure
that those frameworks are working. Each of these processes are not
responsible for one kind of adaptation (not straight forward or simple). First
mechanism: adjustments in macromolecular components
(quantitative/qualitative … concentrations and amounts/types,
respectively). The second mechanism is the modulation strategy, or the
components are being modified, so you don’t have to change quality or
quantity but change environment that they are in (ex: protons). The third
one is adjustments of macromolecular systems, for example hormones.
- An adaptation that occurs quickly is not going to be as “elegant” as one that
occurs over time. 3 time courses: evolutionary or genetic changes,
acclimation (lab situation) or acclimatization (general term, in environment)-
seasonal changes and immediate changes (protein might get phosphorylated
and modify. Direct relationship between stuff that happens inside and
outside of organism (straight line on the graph, x=temp y= body temp).
Poikilotherm= body temperature mimics outdoor temperature and this is
what we call conformity. Homeotherms are regulators, and body
temperature doesn’t change as a function of a change of external
environment (line is horizontal on graph).
- Enantiostasis/allostasis is the maintenance of function in response to
variations or change in external environment. Resistance adaptation
(antifreeze proteins) is changes occurring in extreme conditions. We have to
be careful that we are not comparing completely different organisms that
aren’t appropriate comparisons.
- Enzymes and regulation. Proteins can be used to investigate processes that
organisms are using. Enzymes are marginally stable proteins, they have great
dynamic action, specific role is to convert A->B. 3 characteristics to any
enzyme. Catalysis meaning each one has a catalytic rate at concentration per
unit time. The second one is regulation, where they can have their
concentration regulated, rate etc… Third component is the structure or
confirmation of any enzyme. Any enzyme has a primary structure, secondary
(folds), tertiary (folding of the folded structure), quaternary (subunits that
come together). Most enzymes are part of metabolic pathways but there are
some that are in isolation. How do enzymes work> Boltzmendist distribution
is particular molecules that have a specific amount of energy. Uncatalyzed
reactions take a smaller amount of energy because they already have enough
energy to do it on its own. The catalytic process converts more of those
molecules to product, and moves the free energy line to the left.
- Generally an enzyme is large, however the site at which catalysis actually
occurs which is called the catalytic vacuole, or active site of the enzyme is
relatively small. Once LDH (enzyme) binds the substrates, the confirmation
of the enzyme changes (called induced fit) and there is strain and contortion
which breaks the substrates apart and create products. Size of big enzyme
puts more pressure on substrate to change. Site-directed mutagenesis
changes the protein by mutating certain amino acids in the active site. What
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Document Summary

Looking at a comparison between an animal that lives in low temperature and an animal that lives in high temperatures. Low temp would have a low rate function, and high temp would have a high rate function. (so graph would be a straight line). The reason for that is kinetics, kinetics are temperature sensitive. You can make an animal live at a different temperature, and its rate function would just shift down the graph. They have an ability to adjust; they can do that do that on a seasonal basis, and an on evolutionary basis. Paper that hochachka/somero wrote in 1968 called adaptation of enzymes to temperature and proposed a mechanism to explain this. They suggested that temperature (besides having kinetic effect) also could modify activities, meaning it would directly modify the enzyme and therefore the activity. Hard to define adaptation, because its overused and it occurs at all biological levels. Have an idea of what adaptation is (exam).

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