SGCEP BIOL 1010K
Introduction to Biology I
Spring 2012 Sections
20585 & 20586
Steve Thompson: [email protected]
http://www.bioinfo4u.net/
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Saturday, February 25, 2012
First let’s quickly return to that siliconbased life form, and then we’ll do the
exam review, and metabolism after that.
Since many silicon compounds are quite unstable in water
environments without lots of sulfuric acid, and . . .
Since oxygen based metabolism with silicon produces insoluble
silicon dioxide except at extremely high temperatures, and
since . . .
Ammonia versus water gets around some of these problems,
but oxidizes very rapidly.
It is highly unlikely that there would be enough oxygen gas
around, and even if there was, it would be present in an
atmosphere of strong sulfuric acid vapor and/or ammonia
vapor at very high temperatures! Therefore, no, there’s not
much of a chance that a silicon-based life form and us could
share the same atmosphere. One of us would need a very
sophisticated life support suit.
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Saturday, February 25, 2012
Now the exam review . . . I was quite
disappointed in your performance. Here’s
the questions you did worst on.
5. In the statistical analysis of experimental results:
A. More variation in the data means that the results are more
likely due to the manipulation of the variable
B. Less variation in the data means that the results are more
likely due to the manipulation of the variable
C. The smaller the data sample size, the more robust the
analysis will be
D. Statistics provide absolute confidence of outcome
17. A bond formed bet ween a partially electropositive atom and a
partially electronegative atom is:
A. An ionic bond
B. A nuclear bond
C. A covalent bond
D. A hydrogen bond
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Saturday, February 25, 2012
31. Which of the following statements is not a true characteristic of
Bacterial cells?
A. They have ribosomes
B. They have a cell wall made of cellulose
C. Their primary DNA is circular and ‘loose’ within the cell
D. They may have accessory DNA molecules named plasmids
33. Which of the following statements is not a true characteristic of
Eukaryotic cells?
A. They possess membrane-bounded organelles
B. They are the product of ancient endosymbiotic events
C. Their primary DNA is contained in a membrane-bound nucleus
D. They are more closely related to Bacterial cells than to
Archaeal cell
35. Which of the following is not true about the nucleus?
A. It contains DNA
B. Its nucleolus assembles ribosomes
C. It has pores to let substances in and out
D. It is surrounded by a triple layer of phospholipid bilayers
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Saturday, February 25, 2012
36. The endoplasmic reticulum (ER), whether rough or smooth, does which of
the following things?
A. Produces and/or processes biochemical molecules that exit the ER in
vesicles
B.
Moves biochemical molecules from outside the cell to inside the nucleus
C.
Manufactures DNA and RNA that is moved to the nucleus
D.
Manufactures ribosomes for the cell
45. Which of the following types of cell junctions connects adjacent cells in
animal organs like the stomach where an impervious sheet needs to be
created?
A. Anchoring (also called adhering)
B.
Plasmodesmata
C.
Tight
D.
Gap
49. The simple diffusion form of passive transport is different from active
transport, in that active transport:
A. Requires no energy to maintain
B.
Uses the process of pinocytosis
C.
Requires integral membrane transport proteins
D.
Moves molecules from an area of higher concentration to an area of
lower concentration
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Saturday, February 25, 2012
So now an in-class assignment, this time regarding . . .
Why you did so terrible on this first test!
Remember . . . each sectional exam is only worth 10%, so it’s not that
big of a deal, yet. Think of it as a “wakeup call.”
And, maybe now you’ll realize that you actually will need to work for
this class. And, perhaps you’ll realize just how much the extra-credit
homework component of the class can help . . . as much as an entire
sectional exam!
Seriously, it was a very fair exam . . . only those concepts that I most
emphasized in class were on it. Therefore, . . .
On a piece of paper — name, date, class and section (Bio 1010-20585
on M/W, 1010-20586 on T/Th), and . . .
How can you do better next time? Did you study at all; how much? Are
you printing out my lectures and annotating them as I talk? Are you
then taking those points that I emphasized and making your own study
guide, whether that’s an outline or index cards . . . .
Quietly work on this by yourself for the rest of the class period — come
up with no more than one page — and get it to me as you leave.
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Saturday, February 25, 2012
And now, energy
metabolism
All cells capture and use energy.
There are t wo types of energy:
Potential energy &
Kinetic energy.
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Saturday, February 25, 2012
But first, what’s
“metabolism?”
“The chemical reactions that build and break
down molecules within any cell”
versus . . .
“how fast a person burns food.”
An average human adult burns bet ween 1500
and 2000 Calories per day, just to maintain
heartbeat, temperature, breathing, brain
activity, and other basic life requirements, not
considering digestion or motion.
Where’s all this energy comin’ and goin’?
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Saturday, February 25, 2012
But, what is energy – the ability to do
work, i.e. the ability to move matter.
There are t wo types:
1. Potential energy – stored energy available to
do work, e.g. the energy in an Power bar!
2. Kinetic energy – energy being used to do
work, . . .
e.g. movement, heat, light, and sound.
The calorie is used to measure energy. It’s
defined as the . . .
Energy required to raise 1 gram of water 1° C.
Kilocalorie or Calorie = 1000 calories
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Saturday, February 25, 2012
All sorts of energy going on . . .
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Saturday, February 25, 2012
The laws of
thermodynamics:
First law – the law of
energy conser vation.
Second law – all energy
transformations are
inefficient.
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Saturday, February 25, 2012
First law – law of
energy conser vation
Neither energy nor matter can be created or
destroyed in a closed system (though the t wo
can be converted to one another through
Einstein’s famous E=mc2 relativity equation).
Energy can only be converted to other forms
of energy (other than through E=mc2).
The energy transformations sustaining life
are similar in all organisms (argues for
common ancestry, along with DNA, etc.).
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Saturday, February 25, 2012
Energy transformations
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Saturday, February 25, 2012
Most of life on earth is dependent on
the Sun, ultimately, for all energy,
either directly or indirectly.
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Saturday, February 25, 2012
And then, starting
about 30 years ago, we
discovered that entire
communities of
Bacteria (and Archaea)
lived around
hydrothermal vents
deep in the ocean,
living off of hydrogen
sulfide. These create
mats that begin an
extensive food chain.
Second law – all energy transformations
are inefficient. Heat is always lost . . .
And it’s gone from that system, forever.
Heat is the random motion of molecules —
more motion = more heat.
Entropy is a tendency toward randomness.
Organisms must use incoming energy and
matter to remain organized — they’re an
“open” system. They can only increase in
complexity as long as something else (usu.
the sun) is decreasing in complexity even
more.
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Saturday, February 25, 2012
Chemical reactions
Metabolism — sum of all the reactions in cells. It is . . .
Organized into metabolic pathways. Where the . . .
Product of one reaction becomes the substrate of another.
A linear, chained, and
cyclic pathway . . .
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Saturday, February 25, 2012
Chemical reactions, cont.
They either absorb or release energy:
1. Endergonic reactions (energy enters) —
Require energy to proceed;
Build complex molecules;
e.g. Photosynthesis.
2. Exergonic reactions (energy exits) —
Release energy;
Break apart large, complex molecules;
e.g. Cellular respiration.
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Saturday, February 25, 2012
Endergonic . . .
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Saturday, February 25, 2012
Exergonic . . .
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Saturday, February 25, 2012
Chemical equilibrium
Most reactions can proceed in both directions.
If reactants accumulate, the reaction goes for ward, and visa versa.
At chemical equilibrium, the reaction goes in both directions at the
same rate.
Cells must remain far from equilibrium (that would be death).
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Saturday, February 25, 2012
Oxidation-reduction, a.k.a.
redox reactions, . . .
Transfer energized electrons from one molecule to
another.
Oxidation – lose electrons, release energy.
Reduction – gain electrons, requires energy.
If one molecule is reduced (gains electrons), then
another must be oxidized (lose electrons).
An “electron transport chain” releases small
amounts of energy as electrons are transferred
(and H+ ions are shuttled across a membrane), e.g.
in both:
Photosynthesis and cellular respiration.
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Saturday, February 25, 2012
Electron transport chain in mitochondrion
http://vcell.ndsu.nodak.edu/animations/etc/movie-flash.htm
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Saturday, February 25, 2012
A similar chain in the chloroplast
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Saturday, February 25, 2012
ATP – Adenosine triphosphate
Provides temporary energy storage in all cells.
Adenosine – adenine and ribose
(as in one monomeric unit of RNA), but . . .
Triphosphate – three phosphate groups.
ATP hydrolysis is exergonic and releases
energy:
ATP + H2O → ADP + P + energy.
ATP synthesis is endergonic and stores energy:
ADP + P + energy → ATP + H2O.
Coupled reactions – one provides energy that
drives the other. 24
Saturday, February 25, 2012
Here’s a cartoon:
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Saturday, February 25, 2012
And the way it works:
This reaction “couples” with others in life to make them happen,
e.g. glucose + fructose = sucrose, if ATP can provide the energy.
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Saturday, February 25, 2012
Another coupled reaction:
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Saturday, February 25, 2012
Coupling works through Phosphorylation.
The cell uses ATP as an energy source by
transferring its phosphate group to
another molecule in the coupled reaction.
Two possible effects:
It may energize a target molecule
fueling an endergonic reaction; or . . .
It can cause a protein to change shape.
Humans use around t wo billion ATP
molecules every minute, just to stay
alive!
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Saturday, February 25, 2012
Enzymes — the real workers
Enzymes are proteins that catalyze a
chemical reaction without being
consumed themselves. They do this
through . . .
Lowering the “energy of activation” by
bringing reactants close to each other.
This is the amount of energy required to
start a reaction. Which allows
enzymes to . . .
Increase reaction rates billions of times.
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Saturday, February 25, 2012
They are absolutely essential . . .
And for more than just your laundry!
They do all the factory work in life:
Replicate and transcribe DNA,
Build other proteins (along with
RNA),
digest food and breakdown toxins,
recycle worn-out cellular
constituents, etc., etc. . . .
both in- and outside cells!
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Saturday, February 25, 2012
They work by . . .
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Saturday, February 25, 2012
Here’s an example of an
extracellular enzymatic process:
http://www.bio.fsu.edu/~stevet/VSU/animations/Chapter04/
enzyme_action_final.swf
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Saturday, February 25, 2012
Enzymes are quite
specific . . .
In general — one enzyme, one
substrate, one reaction. This is . . .
Known as “specificity.”
“Active site” ‘lock and key’ ideas, but
do realize the inherent ‘flexibility’ to
the system. More like ‘clouds’ with an
allowable range of shapes.
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Saturday, February 25, 2012
And how they work:
http://www.bio.fsu.edu/~stevet/VSU/animations/Chapter04/
enzymes.swf
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Saturday, February 25, 2012
In review:
Active site — the region where the
reactant (i.e. substrate or ligand) binds.
Usually it’s quite a specific fit (but drugs
[a.k.a. analogs] fit too, they mimic shape).
The active site ‘hugs’ the reactant
forming an enzyme-substrate complex.
The reaction does not alter the enzyme.
Cofactors are nonprotein helpers and are
required by some enzymes, e.g:
Coenzymes/ions/vitamins . . . .
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Saturday, February 25, 2012
Here’s another cartoon:
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Saturday, February 25, 2012
Let’s see how it really looks
— in a serine protease . . .
http://helixweb.nih.gov/cgi-bin/moldraw?1P06
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Saturday, February 25, 2012
Cells precisely control reaction rates.
Pacesetter — the enzyme in a pathway with the slowest
reaction rate sets the rate of the entire pathway. Or . . .
Another way to control speeds —
Negative feedback a.k.a. feedback inhibition:
An excess of a reaction’s product inhibits the enzyme
controlling the product’s formation (very common).
The thermostat example illustrates the concept.
Competitive vs. noncompetitive inhibition.
Positive feedback:
The product activates the pathway, so the reaction
proceeds faster and faster, e.g. fibrin in blood clotting. Or
an example you may be able to relate to better — when
you’ve just made love, and it was really good, you want
more.
This is not nearly as common as negative feedback.
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Saturday, February 25, 2012
Here’s a cartoon:
This example is histidine synthesis in some bacteria.
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Saturday, February 25, 2012
And competitive
[negative] feedback:
This is the
situation with
most drugs! The
drug binds to the
active site better
than the natural
ligand.
Therefore, the
action that the
enzyme (or
receptor) causes
doesn’t occur.
Binds to the enzyme in
the active site
blocking it.
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Saturday, February 25, 2012
Versus noncompetitive [negative] feedback:
Binds to the enzyme
somewhere other than the
active site.
Here a molecule other than the substrate binds to the enzyme
turning it off by changing the shape of the active site.
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Saturday, February 25, 2012
As seen in animation . . .
http://www.bio.fsu.edu/~stevet/VSU/animations/
Chapter04/feedback_inhibition.swf
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Saturday, February 25, 2012
Environmental conditions:
Enzymes are very sensitive (Huh – their feelings get
easily hurt? . . . Nope):
They require a rather narrow range of
environmental parameters. Too hot or too cold
temperature, too high or too low pH, too low or too
high salt concentration, etc., can all alter an
enzyme’s structure, and, hence, function, usually
destroying it.
The name of one such consequence is:
Denaturation — to cause loss of shape and
function by physical means (e.g. cooking denatures
proteins).
The exact conditions depend on the organism and
enzyme, e.g. exceptions like Taq polymerase & PCR.
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Saturday, February 25, 2012
We’ve used up enough of
our energy for now.
Now that we understand what
energy is, and the ways it is used in
life.
And that the most important
energy molecule is ATP.
Let’s see where how
photosynthesis uses the sun to
make ATP and sugar next time.
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Saturday, February 25, 2012