08/23/06

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<h1>Introduction / Information</h1>
<h1>Introduction / Information</h1>
-
*Dr. Stillwell
+
<h2>Dr. Stillwell</h2>
-
**First taught biochemistry in 1980
+
*First taught biochemistry in 1980
-
**Membrane biophysics (structure and function) is his specialty
+
*Membrane biophysics (structure and function) is his specialty
-
**He is an editor of a journal that sees 400+ abstracts each year and excepts about 30.
+
*He is an editor of a journal that sees 400+ abstracts each year and accepts about 30.
-
**He is writing a textbook on membranes.
+
*He is writing a textbook on membranes.
-
**He has terrible health, especially his eyes.
+
*He has terrible health, especially his eyes.
-
*Exams
+
-
**There will be three exams
+
-
**The first exam will be mid-October and will cover some of proteins.
+
-
**The second exam will be near Thanksgiving.
+
-
**Both Exam 1 and Exam 2 are worth 100 points each; the final is worth 200 points.
+
-
**He has the hardest exams ever:
+
-
***The first exam usually sees an average of about 44-49% (class average).
+
-
***The second exam is generally around at 50% class average.
+
-
**Overall class grade of 65% gets curved up to an 'A', generally.
+
-
**Exams are only over class notes!
+
-
**Exams are only over class notes!!
+
-
**Exams are only over class notes!!!
+
-
**The multiple choice sections are the hardest.
+
-
*Generally Good Ideas:
+
-
**Do not get behind.
+
-
**Make [[study groups]].
+
-
**Recopy notes...perhaps by putting them up on this wiki. :)
+
-
**Dr. Stillwell has no office hours; come in whenever.
+
 +
<h2>Exams</h2>
 +
*There will be three exams
 +
*The first exam will be mid-October and will cover some of proteins.
 +
*The second exam will be near Thanksgiving.
 +
*Both Exam 1 and Exam 2 are worth 100 points each; the final is worth 200 points.
 +
*He has the hardest exams ever:
 +
**The first exam usually sees an average of about 44-49% (class average).
 +
**The second exam is generally around at 50% class average.
 +
*Overall class grade of 65% gets curved up to an 'A', generally.
 +
*Exams are only over class notes!
 +
*Exams are only over class notes!!
 +
*Exams are only over class notes!!!
 +
*The multiple choice sections are the hardest.
 +
<h2>Generally Good Ideas</h2>
 +
*Do not get behind.
 +
*Make [[study groups]].
 +
*Recopy notes...perhaps by putting them up on this wiki. :)
 +
*Dr. Stillwell has no office hours; come in whenever.
-
<h1>Early Vertebrate Evolution</h1>
+
<h1>Lecture</h1>
-
*Features that came later in some vertebrates include lungs, teeth, eggs, etc.
+
<h2>The generations of biochemists</h2>
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*Four (4) key features evolved in early vertebrates
+
#1st generation: studied metabolism
-
<h3>1.  Large Brain</h3>
+
#2nd generation: studied molecular biology
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*Necessary to sense environ and move quickly
+
#3rd generation: study dynamics of biology (at the single molecule level)<br />
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*All vertebrates are bilaterally symmetrical with an increased concentration of nervous tissue at the anterior end.
+
*Generalization of biochemistry: the study of composition, organization, structure and function.
-
<h3>2.  Internal Skeleton</h3>
+
*Wohler started this whole business of biochemistry when he used ammonium cyanide to make urea --a product believed at the time to only be producible by living things (which ammonium cyanide obviously is not).  This meant that man may be capable of doing reactions much like what occurs in the body.
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*Can grow without having to molt
+
*Insert paper handout here
-
*Supports larger weight
+
*We can only look for life assuming it is similar to life on Earth (has "the thread of life").
-
<h3>3. Rapid Movement</h3>
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**There is only one thread we know, only one origin.
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*Facilitated by fixed attachment of muscles (to the skeleton)
+
**CHON = the elements here and elsewhere in the solar system.
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<h3>4Large Size</h3>
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*Why is water so important, we'll we'll talk about that next week.
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*Supported by internal skeleton
+
*We cannot imagine life without water, so we assume it is necessary
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*Vertebrates could grow more quickly because they could move to food sources instead of filter feeding (waiting for food to float by).
+
**Second most abundant (non-man-made) liquid is mercury (Hg).
-
 
+
*Rock has been found that was made by bacteria that lives in sulfuric acid.
-
<h1>Focus on Fish</h1>
+
*Europa: a moon of Jupiter; an enormous ball of ice which gravity causes it to crack, then fluid spews up through the cracks and we see that it is yellow.  This makes us think it has organic material in it.
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*Vertebrates have two (2) superclasses, and therefore fish can be broken down by which vertebrate superclass they belong to.
+
*Even if water isn't really necessary for life, we probably won't recognize a form of life that doesn't use water.
-
 
+
<h2>Thread of Life</h2>
-
<h2>1. Jawless Vertebrates (agnatha)</h2>
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*Time frame parameters for life
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*Includes lampreys (suck blood), hagfish, etc.
+
**if it moves too slow we won't be around long enough to observe that it is dynamic; if it is too fast we don't see that it is self-controlled and purposefulEither way, we probably wouldn't recognize forms of life at the extremes of a time scale.
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<h2>2.  Jawed Vertebrates</h2>
+
**we have to use catalysts to make our reactions happen at the correct rate, so we imagine that most forms of life do, also.
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*Includes shark, salmon, humans
+
*Information storage
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*Can injest large food particles.
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**we imagine that all forms of life need something like DNA to keep and pass along information.
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*Jaws evolved from gill supports.
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*Energy currency
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<h3>Two (2) major groups</h3>
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**most forms of life we know use ATP as the energy currency; we imagine that all living things have some sort of comparable currency.
-
<h4>1. The Class Chondrichthyes</h4>
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*Barrier
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*''Chond'' = cartilage, ''ichthyes'' = fish.
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**membranes, life probably needs them.
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*Includes sharks and reyes
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*Limit to the size of single cells
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*Cartilage skeleton (a secondary loss of bone, meaning they had cartilage, then bone, then evolved away from bone again)
+
**There is an upper bound on the size of a single cell because of the rate of diffusion of water. If you assume that each cubic unit necessitates a certain amount of water, then as a cell expands, it becomes harder and harder to get enough water in and out of the cell to fulfill these water demands as surface area does not increase as rapidly as volume in expansion.
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*Only 750 extant species known.
+
*Polymers
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*Well developed sensory system (smell, eyesight, lateral line, etc.)
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**we see that we have many different polymers and assume that most forms of life require such tools.
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<h4>2.  The Class Osteichthyes</h4>
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*Known as boney fish.
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*About 30k extant species
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*Operculum = gill cover that allows stationary position.
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*Have well developed color vision
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**Note coral reef fishes
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<h5>Three groups of boney fish</h5>
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'''1Ray Finned Fish'''
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*Most of the fish we know
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*Salmon, rockfish, goldfish
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'''2. Lobe Finned Fish'''
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*One or two extant species
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*In genus ''Coelacanth''
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*Live deep in the ocean around Southern Africa and Indonesia
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*Lobes are thick and muscular which is a preadaptation for life on land.
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'''3.  Lung Fish'''
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*Found around South America and Africa
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*Fewere than 100 species known.
+
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<h4>Problem with Boney Fish</h4>
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*No trait to unite the group.
+
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*Osteichthyes is paraphyletic.
+
-
<h1>Problems with Existing Rank Taxonomy</h1>
+
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#Many traditional groups are paraphyletic (especially in the vertebrates).
+
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#Rank levels are not equivalent across the group.
+
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#We need more than eight (8) ranks.
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<h4>Solutions</h4>
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*Throw out the ranks and just name all the monophyletic groups.
+
-
 
+
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*video....
+

Current revision as of 16:06, 16 October 2006

Contents

Introduction / Information

Dr. Stillwell

  • First taught biochemistry in 1980
  • Membrane biophysics (structure and function) is his specialty
  • He is an editor of a journal that sees 400+ abstracts each year and accepts about 30.
  • He is writing a textbook on membranes.
  • He has terrible health, especially his eyes.

Exams

  • There will be three exams
  • The first exam will be mid-October and will cover some of proteins.
  • The second exam will be near Thanksgiving.
  • Both Exam 1 and Exam 2 are worth 100 points each; the final is worth 200 points.
  • He has the hardest exams ever:
    • The first exam usually sees an average of about 44-49% (class average).
    • The second exam is generally around at 50% class average.
  • Overall class grade of 65% gets curved up to an 'A', generally.
  • Exams are only over class notes!
  • Exams are only over class notes!!
  • Exams are only over class notes!!!
  • The multiple choice sections are the hardest.

Generally Good Ideas

  • Do not get behind.
  • Make study groups.
  • Recopy notes...perhaps by putting them up on this wiki. :)
  • Dr. Stillwell has no office hours; come in whenever.

Lecture

The generations of biochemists

  1. 1st generation: studied metabolism
  2. 2nd generation: studied molecular biology
  3. 3rd generation: study dynamics of biology (at the single molecule level)
  • Generalization of biochemistry: the study of composition, organization, structure and function.
  • Wohler started this whole business of biochemistry when he used ammonium cyanide to make urea --a product believed at the time to only be producible by living things (which ammonium cyanide obviously is not). This meant that man may be capable of doing reactions much like what occurs in the body.
  • Insert paper handout here
  • We can only look for life assuming it is similar to life on Earth (has "the thread of life").
    • There is only one thread we know, only one origin.
    • CHON = the elements here and elsewhere in the solar system.
  • Why is water so important, we'll we'll talk about that next week.
  • We cannot imagine life without water, so we assume it is necessary
    • Second most abundant (non-man-made) liquid is mercury (Hg).
  • Rock has been found that was made by bacteria that lives in sulfuric acid.
  • Europa: a moon of Jupiter; an enormous ball of ice which gravity causes it to crack, then fluid spews up through the cracks and we see that it is yellow. This makes us think it has organic material in it.
  • Even if water isn't really necessary for life, we probably won't recognize a form of life that doesn't use water.

Thread of Life

  • Time frame parameters for life
    • if it moves too slow we won't be around long enough to observe that it is dynamic; if it is too fast we don't see that it is self-controlled and purposeful. Either way, we probably wouldn't recognize forms of life at the extremes of a time scale.
    • we have to use catalysts to make our reactions happen at the correct rate, so we imagine that most forms of life do, also.
  • Information storage
    • we imagine that all forms of life need something like DNA to keep and pass along information.
  • Energy currency
    • most forms of life we know use ATP as the energy currency; we imagine that all living things have some sort of comparable currency.
  • Barrier
    • membranes, life probably needs them.
  • Limit to the size of single cells
    • There is an upper bound on the size of a single cell because of the rate of diffusion of water. If you assume that each cubic unit necessitates a certain amount of water, then as a cell expands, it becomes harder and harder to get enough water in and out of the cell to fulfill these water demands as surface area does not increase as rapidly as volume in expansion.
  • Polymers
    • we see that we have many different polymers and assume that most forms of life require such tools.
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