Lecture Handouts for this Evening

Take one each of the 3 handouts you will find down front here on the lecture table:

(1) Lecture notes for this evening

(2) Class syllabus

(3) Homework #1

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Course Syllabus:

J G Burr, 08/23/14

BIOLOGY 2311, Sec 501 Introduction to Modern Biology Fall 2014

Tuesday and Thursday, 5:30‑6:45pm, HH 2.402

Syllabus

Instructor: J.G. Burr (FN 3.110; 883‑2508; burr@utdallas.edu)Office Hours: Fri, 3:30-4:30 pm, or by appointmentUndergraduate Teaching Assistants: Ms. Gemma Campos; Ms. Lana Khazma; Ms. Stephanie Mathew; Ms.

Stephanie Nguyen; Ms. Amna Obaid; Ms. Grace An Pham; Mr. Dat Vuong

Required Text: Biological Science, 4th Ed., Scott Freeman (2010), Vol. 1Optional: The Cancer Book, Cooper (1993)

Lecture notes, exam preparation material and other course information will be posted on the course web page:

(http://www.utdallas.edu/~burr/BIO2311) (NOT on eLearning)

This is the first part of a two-semester lecture sequence of introductory biology. There is a co-requisite workshop, BIO 2111. All students enrolled in BIO 2311 must also enroll in a BIO 2111 workshop[1]. The grade for BIO 2111 will be determined by attendance and scores on homework and occasional quizzes, and it will be worth 10% of the overall grade given for BIO 2301. The same grade will be assigned for both BIO 2311 and BIO 2111. If you withdraw from BIO 2311, you must also withdraw from BIO 2111.

The course content of BIO 2311 emphasizes introductory biochemistry, genetics and molecular cell biology. In the first half of the semester, the lectures on these topics will more or less follow the textbook; in the second half of the semester, we will illustrate the concepts of molecular cell biology by delving more deeply than does your text into the molecular basis of cancer.

There will be four exams given in BIO 2311. The exam questions will be a combination of multiple-choice plus brief essay or short-answer questions. Each of the four exams will be worth 20% of the final grade, and each will cover all of the material presented in class since the previous exam (lectures, handouts, and assigned reading). Your exam papers will not be returned, but the answers will be discussed in workshop.

DO NOT MISS THE EXAMS. Makeup exams will be given only in case of a documented emergency and will be MORE DIFFICULT than the regularly scheduled exam. You must contact the Instructor within 24 hours of the missed exam and schedule a makeup exam to be taken immediately.

The prerequisite for this course is successful completion of General Chemistry I & II; the first semester of organic chemistry will ordinarily be taken concurrently with BIO 2311.

See reverse side for lecture schedule_____________________________[1] Medical Schools and most allied health science programs require (along with other courses) a two-semester sequence of introductory biology consisting of two 4-hour courses, each of which has a laboratory component, for a total of 8 semester credit hours of lecture plus laboratory. At UTD, the Biology Department offers two 3-hour lecture courses, Introduction to Modern Biology I and II (BIO 2311, 2312), with associated 1-hour workshops (BIO 2111, 2112) and a separate 2-hour Introductory Biology Laboratory course (BIO 2281), for a total of 10 SCH of lecture plus laboratory.

Lecture 1

BIO 2311.501

Dr. J.G. Burr

Biology 2311 Syllabus (Continued)

Session Lecture Date Subject Assignment

1 1 Aug 26 Tue Origin & evolution of life Chapt. 12 2 Aug 28 Thurs Chemistry of life Chapt. 23 3 Sept 2 Tue Macromolecules (1) Chapt. 3-54 4 Sept 4 Thurs Macromolecules (2) Chapt. 3-55 5 Sept 9 Tue Cell membranes (1) Chapt. 66 6 Sept 11 Thurs Cell membranes (2) Chapt. 67 7 Sept 16 Tue Cell structure (1) Chapt. 78 -- Sept 18 Thurs TEST 1 (Lectures 1-6) The test will cover up to and

through all my lecture material on cell membranes; Chapters 1-6 in your textbook.

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9 8 Sept 23 Tue` Cell structure (2); Respiration (1) Chapt. 7; 910 9 Sept 25 Thurs Respiration (2) Chapt. 911 10 Sept 30 Tue Photosynthesis (1) Chapt. 1012 11 Oct 2 Thurs Photosynthesis (2) Chapt. 1013 12 Oct 7 Tue Cell Division Chapt. 11

pp. 194-204

14 13 Oct 9 Thurs Meiosis Chapt. 1215 14 Oct 14 Tue Mendelian Genetics (1) Chapt. 1316 -- Oct 16 Thurs TEST 2 (Lectures 7-12) (ie, all my lecture material since

‘membranes’ up through and including the topic of cell division) (Chapts 7, 9-11 in textbook)

--

17 15 Oct 21 Tue Mendelian Genetics (2) Chapt. 1318 16 Oct 23 Thurs Mendelian Genetics (3); DNA synthesis, mutation, repair

(1)Chapt. 13; 14

19 17 Oct 28 Tue DNA synthesis, mutation, repair (2) Chapt. 1420 18 Oct 30 Thurs How do genes work? Chapt. 1521 19 Nov 4 Tue Transcription and Translation (1) Chapt. 1622 20 Nov 6 Thurs Transcription and Translation (2) Chapt. 1623 21 Nov 11 Tue Regulation of gene expression: prokaryotes, eukaryotes Chapt. 17, 18

24 22 Nov 13 Thurs Cancer: epidemiology; terminology(for the 3rd edition, Chapt 11, pp 237-240)

Lecture Notes, Chapt 11: pp 206-208

25 -- Nov 18 Tue TEST 3 (Lectures 13 through part of lecture 21; ie, up to and including my lectures on the material in Chapters 12 through 17 in your book) (not including eukaryotic gene regulation, Chapter 18)

--

26 23 Nov 20 Thurs Cancer: chemical carcinogenesis Lecture Notes-- -- Nov 25, 27 (Thanksgiving Holiday) --27 24 Dec 2 Tue The role of viruses in cancer: DNA tumor viruses Lecture Notes28 25 Dec 4 Thurs The role of viruses in cancer: RNA tumor viruses Lecture Notes29 26 Dec 9 Tue TEST 4 (Last part of Lec 21[eukaryotic gene regulation,

Chapter 18 in book] and Cancer Lec’s 22-25)--

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Course home page: http://www.utdallas.edu/~burr/BIO2311/

(I will not be using eLearning for this course.)

J G Burr, 08/18/11

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You can download the PowerPoint lecture notes from our course web page:http://www.utdallas.edu/~burr/BIO2311/(This address is on your syllabus)

You will also (soon, but not yet) be able to get paper copies from the Book Store Copy Center. The Copy Center closes at 5 pm, but since it takes time to print out a full set of notes, and they sometimes get a closing-time rush of customers, you are requested to come in no later than 4:00 pm.

(When I have delivered the printed PowerPoint lecture notes to the Copy Center, I will post an announcement on our course web site.)

J G Burr, , 08/18/11 9

Homework #1 is due in workshops starting this coming Fri, 8/29; then Tue, 9/2 (am, pm); and Wed, 9/3. Since Monday is a holiday, Mon workshop (Sec 013) students: turn in your homeworks in at start of class, Tue evening, 9/2.

J G Burr, , 08/18/11

BIO 2311 Burr

Homework # 1 (Due in workshops the week of Fri, 8/30-Wed, 9/4)

(10 pts) The following 5 multiple-choice questions are worth 2 points each:

1. Cosmologists have determined that the age of our universe (time since the big bang) is

approximately ______ years: 1) 7 billion 2) 14 billion 3) 37 billion 4) 1.4 trillion

2. Astronomers estimate that our sun is approximately _______ billion years old, and that it will become a red giant in approximately another ________ billion years: 1) 1, 5 2) 5, 10 3) 10, 20 4) 5, 5

3. When a star the size of our sun “goes nova” it blows off a cloud of hydrogen, helium, carbon and ________; stars 25-fold larger than our sun can make elements up to the atomic mass of ________ by fusion reactions, before they “go supernova.” 1) oxygen, iron 2) silicon, uranium, 3) oxygen, silicon 4) argon, nickel.

4. The earliest fossil remains of cells are found in rocks that have been dated to approximately ________ years old. 1) 100 million 2) 1 billion 3) 3.5 billion 4) 20 billion

5. 250 million years ago, the present-day continents were all part of a large single continent called: 1) Gondwana 2) Omniterra 3) Laurasia 4) Pangea

If you are enrolled in my lecture section (Dr. Burr, BIO 2311.501) you must be enrolled in one the following Workshop sections:

Sec 001, 002: Tue, 4:00 pm

Sec 003, 004: Tue, 8:30 am

Sec 005: Wed, 1:00 pm

Sec 006: Fri, 1:00 pm

Sec 013: Mon, 1:00 pm

(Workshop sections 007, 008, 009, 010, 011, and 012 are only for students enrolled in Dr Srikanth’s Intro Biology lecture course, BIO 2311.001, that meets at 11:30 am on Tue, Thurs.) If you mistakenly enrolled in one of these you must drop/add.

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Over the course of the coming semester, we’re going to talk about evolution, cells, a bit of basic biochemistry and genetics, and then conclude with some lectures on the molecular basis of cancer.

J G Burr, ,08/18/11

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We’re going to start off by talking in a general way about what we know of the origin and evolution of life on our planet. This means we’ll need to get into a little bit of chemistry, physics, and even a bit of geophysics.

J G Burr,08/18/11

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Lets start off with a little chemistry review:

Everything is made of atoms, and there are some 112 different kinds of atoms.

J G Burr, 08/23/14

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What kind of atoms, for example, is water made of?

J G Burr, 08/23/14

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As you well know, water (H20) is a molecule made of two hydrogen atoms plus one oxygen atom:

Water is a liquid at room temperature because the (δ+)H atoms on one water molecule are electronically attracted to the (δ-)O atoms on other water molecules, forming “hydrogen bonds.”

J G Burr, 08/23/14

The electronic bond (shared electrons) between O and H is a covalent bond, with polar character. Oxygen is much more electronegative than hydrogen, and the electron from hydrogen spends more time around the oxygen nucleus.

(δ+)H

(δ-)O

A hydrogen bond is a ‘weak’ bond; it is much weaker in strength than a covalent or an ionic bond, but stronger than a van der Waals interaction.

In other words, water is a dipolar molecule, capable of forming hydrogen bonds with up to 4 other partner water molecules

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Atoms have a nucleus with positively charged protons (plus in all cases except hydrogen, some neutrons), orbited by negatively charged electrons:

Hydrogen is the simplest atom with just one proton in the nucleus, and one orbiting electron

Helium is the next simplest atom with two protons in the nucleus, and two orbiting electrons. It also has two uncharged things the same size as protons in its nucleus, called neutrons. (Under certain extraordinary circumstances, a proton can give off a positron + a neutrino to become a neutron!)

Protons

Neutrons

electrons

J G Burr, 08/23/14

Hydrogen

Helium

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Where do all these kinds of atoms (the elements listed in the Periodic Table) come

from?

J G Burr, 08/23/14

They have all been made inside of stars.

All the different elements that make up the material in the furniture in this room; the room itself, and all the different kinds of atoms that make up your bodies: all of this was created billions of years ago in the furnace of stars that existed at an earlier time in our galaxy, long before our own star (the sun) was formed.

J G Burr, 08/23/14

(In my experience, some of you will start to become a bit anxious as we go through the material that I will now start talking about. (“What the heck? I thought this supposed to be a Biology course.”) Do not be afraid: The detailed information that follows in slides #14 - #26 will “not be on the test.” We are going to go through it because, in my opinion, a Biology major should have at least been briefly exposed to this general scientific information!)

In the center of stars, the huge force of gravity compresses hydrogen nuclei (protons) so tightly together that they begin to fuse to form helium nuclei. 4 protons fuse to form a helium nucleus:

4 Hydrogen nuclei (protons)

A helium nucleus

(2 protons + 2 neutrons)

This released energy is what makes the sun hot and bright, and it staves off further gravitational collapse.

J G Burr, 08/23/14

(Two of the protons each release a positron and a neutrino, to become a neutron.)

neutrinos

positrons

(A helium nucleus has a little less mass than the combined mass of the four starting protons; the difference in mass is released as Energy.) (Remember, E=mc2)

One of the two neutrons

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Our sun is fusing (“burning”) hydrogen to make helium, and will continue doing so for about another 5 billion years. Basically, our sun is a long, continuous, sustained hydrogen bomb explosion!

Our sun

Hydrogen bomb

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The energy released in the center of the star by the fusion of hydrogen nuclei to form helium provides an outward force that counteracts the inward force of contraction due to gravity. Consequently, once ‘ignition’ has occurred, the star remains at a more or less constant size over time, as long as it is ‘burning hydrogen.'

J G Burr, 08/23/14

Inward force due to Gravity

Outward force due to energy of fusion reaction

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As our sun synthesizes helium, this helium accum-ulates in the center of our sun.

Sun ‘burning’ hydrogen (fusing protons) to form helium

Sun ‘burning’ helium to form carbon (fusing helium nuclei to form carbon nuclei)

Eventually our sun will run short of hydrogen, and then it will start fusing helium nuclei together to form carbon:

Growing helium core

H H

J G Burr, 08/23/14

After protons are ‘used up’, gravitational collapse begins again, and then with the greater internal compression, the star starts fusing helium nuclei to form carbon nuclei.

Now, growing carbon core

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“Red giant” Sun burning helium to

form carbon

The energy released from burning helium to make carbon is much greater than the previous fusion reaction; consequently, our sun will then become even hotter, and expand to become what is known as a “red giant”:

H

J G Burr, 08/23/14

Sun burning hydrogen to form helium

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When our sun becomes a red giant it will engulf the earth, and the earth will be toast. (But don’t worry, this event is 5 billion years away.)

J G Burr, 08/23/14

The size of our

Sun at present

The size our Sun will be when it becomes a red giant

Five billion years after our sun has become a red giant, it will undergo a final gravitational contraction to become a small, hot, “white dwarf”. At that time, it will blow off a cloud of hydrogen, helium, carbon and oxygen molecules (a “nova” outburst, forming a “planetary nebula”).

J G Burr, 08/23/14

White dwarf star. Fusion reactions no longer occur in its center. It glows from left-over heat.

(White dwarf stars consist of tightly packed carbon and oxygen atoms (mostly); very dense: 1 tsp = approximately 1 ton.)

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All medium-sized stars like our sun end as white dwarfs in the center of a ring nebula. (Eventually the white dwarf will cool off and become a cold, dead cinder, called a “black dwarf”. )

J G Burr, 08/23/14

White Dwarf remnant star

“Ring Nebula”

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Stars bigger than our sun (10x bigger) follow a different fate. After forming carbon, large stars will successively form neon, then oxygen, silicon, and finally iron:

J G Burr, 08/23/14

(All the galaxies we find in the Universe now were formed by about a billion years after the Big Bang. Large iron-forming stars like this were more common in the young galaxies.)

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When all the silicon is depleted, then there is no more fusion-released energy to stave off the gravitational collapse of the star. The star collapses, and then explodes outwards. This is called a “Super Nova”:

J G Burr, 08/23/14

The energy of a hundred billion suns is released in an instant!

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(In the case of stars of size between 10 and 25 times the mass of our sun, the residue left after a supernova explosion consists of close-packed neutrons; it is called a neutron star; with stars of mass greater than 25x that of our sun, the neutrons collapse in the face of the huge gravitational field and a Black Hole forms after the supernova event.)

J G Burr, 08/23/14

Black hole

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The huge energies associated with supernova explosions result in the synthesis of all the rest of the elements in the periodic table.

The cloud of elements blown out into space as “cosmic dust” after a nova event is called a “nebula”:

The “Crab nebula”: (in our Milky Way galaxy)

J G Burr, 08/23/14

Neutron star (or black hole) left in center of the nebula

(Neutron stars are incredibly dense. 1 tsp = approx. 50 million tons!)

(They are essentially one immense atomic nucleus.)

“Cosmic dust”

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The “cosmic dust” from supernovas can then collapse again gravitationally to form new second generation suns with planetary systems like ours. All the elements like iron, silicon, carbon, oxygen, silver and gold we find on our planet were made in a sun many billions of years ago. Our planet, and we ourselves, are literally made of “stardust.”

J G Burr, 08/23/14

Dust & gas left from a supernova explosion

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Our sun and planets formed from the nebular remains of earlier supernova explosions in our galaxy.

(a) Under the influence of gravity, this cosmic dust began to collapse into a rotating, disk-shaped mass of dust and gas.

(b) The center became super-heated and formed a new star (our sun) (burning hydrogen)

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(c) In the rotating disk of dust around the new sun, individual planets began to form, again by the action of local gravitational attraction. (We now have ways to look for planets around other suns in our galaxy, and we have found many stars with planets around them.)

(d) By about 5 billion years ago, our solar system was formed

Early Earth (“3rd Rock from the Sun”)

Sun

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J G Burr, 08/23/14

Our sun is one of a 100 billion other stars in the Milky Way galaxy, located about here

The Big Bang (the birth of our Universe) occurred 13.7 billion years ago. The first stars were formed from the hydrogen and helium created by the Big Bang within a couple of hundred million years after the event. Our galaxy, and all the 100 billion galaxies in the universe, were formed within the first billion years after the Big Bang. Again, our sun is a second generation star, formed about 5 billion years ago from the supernova dust of a first generation

star that blew up in our galaxy.

The Milky Way galaxy

Our planet and moon rotating around the sun.

Our star, the sun.

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More detail on formation of the earth:1. Shows the earth growing in size as

planetesimals accreted from the nebular cloud collide with the growing earth.

2. As the mass of the earth grew, so did its gravitational force, and the earth began to compress itself into a smaller and denser body

3. In the third step, the compression in the interior began to heat up this core, and the interior began to melt. (Actually, most of the heat was then and is now generated by the radioactive decay of certain heavy elements.)

4. Because iron is the heaviest of the common elements that make up the earth, great globs of molten iron fell by gravity into the center of the earth.

J G Burr, 08/23/14

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Early in the history of the earth, the moon was formed after a glancing collision between the earth and a Mars-sized object.

This is a picture of the earth and moon, shortly after they had formed and were beginning to cool off, about 4.5 billion years ago:

J G Burr, 08/23/14

The moon was formed by material from the outer “mantle” of the early earth, blown off into space by the collision.

Consequently, the moon, unlike the earth, does not have a core of iron.

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The earth still has an iron core. (Solid iron in the center, molten iron above that.)

Above that iron core is hot, molten rock, called the “mantle”.

The heat in the interior of the earth comes mostly from the radioactive decay of uranium, potassium and thorium isotopes.

The outermost layer of cold, hard rock is called the crust.

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Because heat rises, and cool, dense mantle will sink by gravity, the hot, molten mantle moves in a circular way called “convection”.

The convection of the underlying mantle causes movement of outermost layer of crust.

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Upwelling hot lava

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The surface of the earth consists of moving plates of crust. The movement of these surface plates is called plate tectonics.

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North America, South America, Africa & Europe are all on different moving plates of crust. This is the way these plates are now:

(But because they move around on the surface of the earth, they used to be in different places.)

N. America

S. America

Africa

Europe

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This is the way the surface of the earth used to look, long ago:

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This is the way the its been changing over time, over the course of the last 250 million years:

The period of time from 65 million years ago to about 250 million years ago is know as the Mesozoic period; it was the Age of Dinosaurs

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The supercontinent, “Pangea”

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This is the way the way it will look 50 million years from now:

J G Burr, 08/23/14

(Notice a subduction trench has formed along the eastern coast of the Americas.)

Baja California is up near Alaska!

The Mediterranean Sea has become a mountain range!

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This is the way the way it is predicted to look 250 million years from now!

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These plate movements explain why we see fossil remains of the same ancient animal restricted to certain areas of both Africa and South America:

J G Burr, 08/23/14

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How do we know that the solar system (Sun and Earth and the other planets) formed 4.5 billion years ago?

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Answer: because of the known decay rate of certain radioactive elements, like uranium isotope U238.

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The Uranium isotope U238 undergoes radioactive decay with a half-life of 4.5 billion years, to form a stable ‘daughter isotope’ of Lead, Pb206.

Initially, a piece of rock contains only U238 atoms.

As time goes by, it contains a mixture of U238 plus a lead isotope (Pb206 ) (shown in grey)

So by measuring the amounts of uranium (U238) and lead (Pb206) isotopes in a piece of rock, we can tell how old a rock is.

J G Burr, 08/23/14

(Remember, uranium (U238) undergoes radioactive decay to form Lead, with a half-life of 4.5 billion years)

In the oldest rocks, we find approximately equal amounts of U238 and Pb206. This means one “half-life” of U238

elapsed since the rock was formed. A half-life of U238 is 4.5 billion years, so the rock is 4.5 billion years old.

U238

Pb206

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Its hard to find rocks this old on earth, but many meteorites have been analyzed, and found to be the same age (4.5 billion years old).

J G Burr, 08/23/14

Meteorites come from small rocky bodies called “asteroids”. Asteroids orbit the sun in a belt that lies between Mars and Jupiter, and were formed at the same time as the sun and planets. Occasionally these rocks are jostled out of their orbits, fall in towards the Sun and collide with the earth.

Asteroid belt

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So if the earth is 4.5 billion years old, how long has there been life on earth?

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Answer: the earliest fossil remains of cells are found in sedimentary rocks that are about 3.5 billion years old.

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Chain of cells

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And rocks 3.8 billion years old have been found with numerous specks of carbon which appear to be carbonized cells. We deduce that these carbon specks might well be the remains of cells because of the characteristic 12C/13C ratios they contain1.

J G Burr, 08/23/14

1Living organisms fix the 12C isotope ( as 12CO2) preferentially over the 13C isotope ( as 13CO2), leading to enriched 12C/13C ratios.

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How did life start on earth?

J G Burr, 08/23/14

We don’t exactly know.

We’ll discuss what we do know about this topic next

lecture.