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(2) Class syllabus
(3) Homework #1
(4) Info about lecture notes availability
BIO 2311.501
Dr. J.G. Burr
Lecture 1
Course Syllabus:
BIOLOGY 2311, Sec 501
Introduction to Modern Biology
Fall 2015
Tuesday and Thursday, 5:30-6:45pm, HH 2.402
Biology 2311 Syllabus (Continued)
Session
Lecture
Date
Subject
Assignment
1
2
3
4
5
6
7
8
1
2
3
4
5
6
7
--
Aug 25 Tue
Aug 27 Thurs
Sept 1Tue
Sept 3 Thurs
Sept 8 Tue
Sept 10 Thurs
Sept 15 Tue
Sept 17 Thurs
Origin & evolution of life
Chemistry of life
Macromolecules (1)
Macromolecules (2)
Cell membranes (1)
Cell membranes (2)
Cell structure (1)
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.
Chapt. 1
Chapt. 2
Chapt. 3-5
Chapt. 3-5
Chapt. 6
Chapt. 6
Chapt. 7
--
9
10
11
12
13
8
9
10
11
12
Sept 22 Tue`
Sept 24 Thurs
Sept 29 Tue
Oct 1 Thurs
Oct 6 Tue
Cell structure (2); Respiration (1)
Respiration (2)
Photosynthesis (1)
Photosynthesis (2)
Cell Division
14
15
16
13
14
--
Oct 8 Thurs
Oct 13 Tue
Oct 15 Thurs
Meiosis
Mendelian Genetics (1)
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)
Chapt. 7; 9
Chapt. 9
Chapt. 10
Chapt. 10
Chapt. 11
pp. 194-204
Chapt. 12
Chapt. 13
--
17
18
15
16
Oct 20 Tue
Oct 22 Thurs
Mendelian Genetics (2)
Chapt. 13
Mendelian Genetics (3); DNA synthesis, mutation, repair (1) Chapt. 13; 14
19
20
21
22
23
17
18
19
20
21
Oct 27 Tue
Oct 29 Thurs
Nov 3 Tue
Nov 5 Thurs
Nov 10 Tue
DNA synthesis, mutation, repair (2)
How do genes work?
Transcription and Translation (1)
Transcription and Translation (2)
Regulation of gene expression: prokaryotes, eukaryotes
Chapt. 14
Chapt. 15
Chapt. 16
Chapt. 16
Chapt. 17, 18
24
22
Nov 12 Thurs
Cancer: epidemiology; terminology
(for the 3rd edition, Chapt 11, pp 237-240)
Lecture Notes,
Chapt 11: pp 206-208
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.
25
--
Nov 17 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)
--
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.
26
-27
28
29
23
-24
25
26
Nov 19 Thurs
Nov 24, 26
Dec 1 Tue
Dec 3 Thurs
Dec 8 Tue
Cancer: chemical carcinogenesis
(Thanksgiving Holiday)
The role of viruses in cancer: DNA tumor viruses
The role of viruses in cancer: RNA tumor viruses
TEST 4 (Last part of Lec 21[eukaryotic gene regulation,
Chapter 18 in book] and Cancer Lec’s 22-25)
Lecture Notes
-Lecture Notes
Lecture Notes
--
Syllabus
Instructor: J.G. Burr (FN 3.110; 883-2508; [email protected])
Office Hours: Fri, 3:30-4:30 pm, or by appointment
Undergraduate Teaching Assistants: Ms. Rajvi Bhagat; Mr. Jimmy Cheng; Ms. Rachael Couch; Ms. Anne Duong; Mr.
Karthik Hullahalli; Ms. Lu-Yi (Ruby) Kang; Mr. Mehraban Kavoussi; Ms. Rishika Navlani
Required Text:
Optional:
Biological Science, 4th Ed., Scott Freeman (2010), Vol. 1
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.
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.
J G Burr, 08/23/15
Course home page: http://www.utdallas.edu/~burr/BIO2311/
(I will not be using eLearning for this course.)
3
J G Burr, 08/23/15
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, 08/23/15
Important note on Workshops and Workshop
section enrollment:
If you are enrolled in this lecture
There were no workshops
yesterday or today, but
workshops will commence
starting tomorrow (Wednesday)
afternoon (2111.005, 4 pm), and
then of course Thurs and Friday
& on into next week.
Sec 005: Wed, 1:00 pm
Sec 014: Thurs, 8:30 am
Sec 006: Fri, 1:00 pm
section (Dr. Burr, BIO 2311.501)
you must be enrolled in one
the following 8 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
Sec 014: Thurs, 8:30 am
(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, which
meets at 11:30 am on Tue, Thurs.) If you
mistakenly enrolled in one of these you must do a
drop/add and enroll in one of my workshops!
J G Burr, 08/23/15
For students in Workshop section 006, Homework #1 is due this coming
Friday (8/28) in your workshop. The rest of you will turn it in at the start
of your own workshops next week.
It will be the same for homework #2 next week except, since Monday
9/7 is a holiday, Monday workshop students (Sec 013) will turn in their
homeworks that week on Tue evening, 9/8, at the start of class.
BIO 2311 Burr
Homework # 1 (Due in workshops the week of Fri, 8/28-Wed, 9/3)
(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
J G Burr, 08/23/15
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.
7
J G Burr, 08/23/15
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.
8
J G Burr, 08/23/15
Lets start off with a little chemistry review:
Everything is made of atoms, and there
are some 112 different kinds of atoms.
9
J G Burr, 08/23/15
What kind of atoms, for example, is
water made of?
10
J G Burr, 08/23/15
As you well know, water (H20) is a molecule made of two
hydrogen atoms plus one oxygen atom:
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.
In other words, water is a dipolar
molecule, capable of forming hydrogen
bonds with up to 4 other partner water
molecules
(δ-)O
(δ+)H
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.”
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.
11
J G Burr, 08/23/15
Atoms have a nucleus with positively charged protons
(plus in all cases except hydrogen, some neutrons),
orbited by negatively charged electrons:
Neutrons
Hydrogen
electrons
Helium
Protons
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!)
12
J G Burr, 08/23/15
Where do all these kinds of atoms (the elements
listed in the Periodic Table) come from?
13
J G Burr, 08/23/15
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.
(In my experience, some of you will start to become a bit worried 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.”)
Fear Not: The detailed information that follows in slides #14 - #26
will “not be on the test.” We are going to go through it because I
believe that a Biology major should have been at least briefly
exposed to this basic information!)
J G Burr, 08/23/15
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)
positrons
One of the
two neutrons
neutrinos
This released energy
is what makes the
sun hot and bright,
and it staves off
further gravitational
collapse.
A helium nucleus
(2 protons + 2 neutrons)
(Two of the protons each release a positron
and a neutrino, to become a neutron.)
(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)
J G Burr, 08/23/15
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
16
J G Burr, 08/23/15
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 Inward
force due
hydrogen.'
to Gravity
Outward
force due
to energy
of fusion
reaction
17
J G Burr, 08/23/15
As our sun
synthesizes helium,
this helium accumulates in the center
of our sun.
Eventually our sun will
run short of hydrogen,
and then it will start
fusing helium nuclei
together to form carbon:
Now, growing carbon core
Growing helium core
H
H
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.
Sun ‘burning’ hydrogen
(fusing protons) to form
helium
Sun ‘burning’ helium to form
carbon (fusing helium nuclei
to form carbon nuclei)
18
J G Burr, 08/23/15
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
Sun burning hydrogen to
form helium
“Red giant” Sun
burning helium to
form carbon
19
J G Burr, 08/23/15
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.)
The size of our
Sun at present
The size our Sun
will be when it
becomes a red
giant
20
J G Burr, 08/23/15
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”).
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.)
J G Burr, 08/23/15
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”. )
“Ring Nebula”
White Dwarf
remnant star
22
J G Burr, 08/23/15
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:
(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.)
23
J G Burr, 08/23/15
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”:
The energy
of a hundred
billion suns is
released in
an instant!
24
J G Burr, 08/23/15
(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.)
Black hole
25
J G Burr, 08/23/15
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)
“Cosmic dust”
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.)
26
J G Burr, 08/23/15
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.”
Dust & gas left from a
supernova explosion
27
J G Burr, 08/23/15
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, diskshaped mass of dust and gas.
(b) The center became superheated and formed a new star
(our sun) (burning hydrogen)
28
J G Burr, 08/23/15
(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
Sun
Early Earth (“3rd Rock from the Sun”)
29
J G Burr, 08/23/15
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.
Our star,
the sun.
Our sun is
one of a
100 billion
other stars
in the
Milky Way
galaxy,
located
about here
The Milky Way galaxy
Our planet and
moon rotating
around the sun.
30
J G Burr, 08/23/15
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.
31
J G Burr, 08/23/15
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:
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.
32
J G Burr, 08/23/15
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.
33
J G Burr, 08/23/15
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.
Upwelling hot lava
34
J G Burr, 08/23/15
The surface of the earth consists of moving plates
of crust. The movement of these surface plates is
called plate tectonics.
35
J G Burr, 08/23/15
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
Europe
Africa
S. America
36
J G Burr, 08/23/15
This is the way the surface of the earth
used to look, long ago:
37
J G Burr, 08/23/15
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
The supercontinent,
“Pangea”
38
J G Burr, 08/23/15
This is the way the way it will look 50 million
years from now:
(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!
39
J G Burr, 08/23/15
This is the way the way it is predicted
to look 250 million years from now!
40
J G Burr, 08/23/15
These plate movements explain why we
see fossil remains of the same ancient
animal restricted to certain areas of both
Africa and South America:
41
J G Burr, 08/23/15
How do we know that the solar system (Sun
and Earth and the other planets) formed
4.5 billion years ago?
42
J G Burr, 08/23/15
Answer: because of the known decay rate
of certain radioactive elements, like
uranium isotope U238.
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)
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.
43
J G Burr, 08/23/15
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.
Pb206
U238
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.
(Remember, uranium (U238) undergoes radioactive decay to form Lead,
with a half-life of 4.5 billion years)
J G Burr, 08/23/15
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).
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
45
J G Burr, 08/23/15
So if the earth is 4.5 billion years old, how
long has there been life on earth?
46
J G Burr, 08/23/15
Answer: the earliest fossil remains of
cells are found in sedimentary rocks
that are about 3.5 billion years old.
Chain of cells
47
J G Burr, 08/23/15
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.
Living organisms fix the 12C isotope ( as 12CO2) preferentially over
the 13C isotope ( as 13CO2), leading to enriched 12C/13C ratios.
1
48
J G Burr, 08/23/15
How did life start on earth?
We don’t exactly know.
We’ll discuss what we do know
about this topic next lecture.
49
J G Burr, 08/23/15