111 BS Cells and Molecules
Spring 2010 section 001
Co-instructors
Dr.Will Kopachik Dr. Ron Patterson
(Dept. of Zoology)
(Dept. of Microbiology
and Molecular Genetics)
Dr. Will Kopachik (co-instructor)
Office:39 Natural Science Building
e-mail: [e-mail]
Phone: 3-5166
Office hours: Mondays 1:30 to 4:00 without
appointment. Contact me re: other times.
Weekly question-answer sessions: 3:00 to 4:00
Fridays in Natural Science room 128.
Special reviews before exams (usually the day
before to be announced later.
Dr. Ron Patterson (co-instructor)
Office: 4198 BPS Bldg.
Phone: [phone]
Email: [e-mail]
Office hours: Monday noon to 2:00
Lecture TA: Jameel Al-Haddad,
[e-mail](for absences,help with course
content, clickers)
Shirley Reuther (Bio Sci Program office, 203 N.
Kedzie; 432-1316).See her for administrative
questions (drops, adds, exam waivers).
Information on BS 111 class schedule
topics, text reading assignments, examination
dates, strategies for success are given in the
ANGEL website.
1. The ANGEL site will be used for posting
syllabus, announcements, Powerpoint slides,
lecture study guides, practice exams.
2. The required textbook is by Campbell
and Reece, Biology 8th ed. Benjamin
Cummings.
3. You will need an iClicker to get credit for in
class participation.
Strategies for doing well
Do textbook reading and look at slides
before class.
At lecture add notes. Participate in the
clicker quizzes.
Soon after rewrite notes, complete study
guides. For questions see one of us.
Plan well ahead for the exams.
Read the syllabus (suggestions for improved
study habits)
Please do not disrupt your fellow students by
use of cell phones, music players, laptops
including your game, gambling, and social
networking addictions.
Please keep your viral or bacterial afflictions
with you at all times. Stay home if you are
sick; you will not be unduly disadvantaged.
Lectures are on Camtasia, review sessions
are available, waivers for clicker points are
possible.
A message to graduating seniors:
Youve put off BS 111 perhaps because you consider it will
be your capstone and highlight course at MSU.
Here are some answers to questions we hope you will not
be asking the last week of class:
1. No, there is no extra credit by writing a term paper nor
can you retake or have an exam waived because you
believe the grade doesnt show how well you actually can
do.
2. No, we cannot pass you with a less than 47 % average
even if this is: the last class you need, you have a plum of a
job waiting, youre out of money, your apartment lease is
expiring or youre getting married and moving away).
3. No, there is nothing to be done now. There were some
things that could have been done earlier in the semester
DATE
POINTS
Exam 1
(W) Feb. 10
2
(W) March 3
3
(W) April 7
Final Exam
(Th) May 6
Exam Points
Clicker Points
Total Course Points
% of Total Possible Points
83 100
77 82
71 76
65 70
59 64
53 58
47 52
0 46
100
100
100
200
500
30
530
Grade for Course
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.0
This room 1281 Anthony and C102 Wilson will be used for the exams.
Before the exam you will be told which room to go.
BS 111 covers subcellular and cellular
biology. Topics include:
Structure, function and synthesis of
macromolecules
Cell structure and function
Cellular generation and use of energy
Intracellular and extracellular signals
Cell reproduction
The replication, transmission and
expression of genetic information in viral,
prokaryotic and eukaryotic organisms.
DNA technology and Genomics
The major points will be in blue on the
slides.
Introduction/Chemical Bonds
The most important
hypothesis in all of
biology is that everything
that animals do, atoms
do. In other words, there
is nothing that living
things do that cannot be
understood from the point
of view that they are
made of atoms acting
according to the laws of
physics.
Richard P. Feynman
Nobel Prize in Physics 1965
tRNA is the one molecule that adapts the
nucleic acid and amino acid languages.
Transfer RNA structure
BS 111 covers the areas in red which form a
foundation for biological understanding at all other
levels.
Biological Discipline
Level of Analysis
Population Biology
Organismal Biology
Physiology
Developmental Biology
Cell Biology
Biochemistry
Molecular Biology
Ecosystems
Organisms
Organs and tissues
Embryos
Cells and organelles
Macromolecules
Nucleic acids and
genes
The hierarchy of biological order from atom to organism
BS 111
topics
I. A Big Picture view of unifying
principles in cellular life
A. The rules of physics and chemistry govern
life.
B. All cells use the same set of core
________________molecules in an
aqueous (water-based) solution.
-~1000 molecules (glucose, amino acids,
nucleic acids, ATP, etc.
I. A Big Picture view of unifying
principles in cellular life
A. The rules of physics and chemistry govern
life.
B. All cells use the same set of core
hydrocarbon-based molecules in an
aqueous (water-based) solution.
-~1000 molecules (glucose, amino acids,
nucleic acids, ATP, etc.
When available only one enantiomer
(optical isomer) is used:
e.g. Only left-handed, not right-handed,
amino acids are used.
Levo=L
Dextro=D
= optical isomers
When available only one ___________
(optical isomer) is used:
e.g. Only left-handed, not right-handed,
amino acids are used.
Levo=L
Dextro=D
= optical isomers
Water is the
universal solvent
for life on earth.
NH3 is a good solvent, but not for us!
Macromolecules are constructed of ________
(linear molecules made by linking simpler
molecules (e.g. proteins are amino acid
polymers).
Macromolecules are constructed of polymers
(linear molecules made by linking simpler
molecules (e.g. proteins are amino acid
polymers).
C. A core of multi-step biochemical
pathways of synthesis (anabolism), use
and breakdown (catabolism) of molecules
is similar in all cells.
The black points
represent key
biochemicals and
the green arrows
show pathways
interconnecting
them in a yeast
cell.
C. A core of multi-step biochemical
pathways of synthesis (__________), use
and breakdown (__________) of
molecules is similar in all cells.
The black points
represent key
biochemicals and
the green arrows
show pathways
interconnecting
them in a yeast
cell.
The catabolism of various food molecules
D. All cells are
bordered by a
phospholipid
membrane
making possible a
compartment of
the core
molecules.
Comparison of chemiosmosis in mitochondria and chloroplasts
Mitochondrion
and chloroplast
are example of
organelle
compartments.
D. ContinuedOnly two cell
types exist.
_________ ____:two
border membranes,
no nucleus, limited
internal membranes.
_________ ___: single
outer membrane but
extensive internal
membrane-bordered
organelles, with a
nucleus
D. ContinuedOnly two cell
types exist.
Prokaryotic cells:two
border membranes,
no nucleus, limited
internal membranes.
Eukaryotic cells: single
outer membrane but
extensive internal
membrane-bordered
organelles, with a
nucleus
Which is a potential question topic on an
important point for the first exam?
A. Recalling verbatim Feynmans introductory
quote.
B. That BS 111 covers cells, macromolecules
and genes.
C. All biological macromolecules are
polymers.
D. A high concentration of H+ ions across the
thylakoid to stroma space is used to make
ATP.
What is the value of a membranebounded compartment to a cell?
A. Can concentrate interacting molecules
and thus make reactions more efficient.
B. Can separate molecules and reactions
from those that are interfering or nonproductive to a biochemical reaction.
C. Can use it to store water.
D. A and B above are correct.
E. A, B and C above are correct.
E. Adenosine triphosphate (ATP)
is universally used as energy currency.
You do not have to know the ATP structure at this time.
WARNING: The many new terms with specific
meanings used in each lecture will add up
quickly (to about 500!). Think of this as a
vocabulary course where you will have to learn
these terms as you encounter them. Try making
flash cards.
Acronyms: These will be used a lot (e.g. DNA
and RNA). For new terms I will briefly use the
full term, e.g.
Adenosine triphosphate, but then for
convenience I will use ATP.
F. All cells, and viruses, use
polymers of nucleic acids for inheritable
genetic information.
The ______ ______of
information flow
occurs in all cells.
DNA
RNA
Protein
F. All cells, and viruses, use
polymers of nucleic acids for inheritable
genetic information.
The Central Dogmaof
information flow
occurs in all cells.
DNA
RNA
Protein
G. All cells must arise from a
preexisting cell.
Figure 1.7
A daughter cell gets
from its parent cell
the necessary
genetic and paragenetic (spatial,
organizational)
information plus a
high energy state.
Themes for understanding cellular
life
1. Energy:
2. Matter:
3. Organization:
4. Information:
II. Short review of the chemical
context of life.
A longer review of essential inorganic
chemistry is found in Ch. 2 (optional reading).
Here we will focus on:
A. Elements
B. Bonds
C. Water
D. Carbon
A.Elements in biology:
96% are C,O,H,N; rest mainly P,S,Cl,Ca,K
(plus 16 trace elements): 25 in total
e.g. Mg (magnesium) a trace element is
required for all DNA polymerases (enzymes
which copy DNA)
I (iodine) is required for
thyroxin, a hormone made by
the thyroid gland
Atomic number = protons = 11Na
Atomic weight (mass) = protons and
neutrons
= 23Na
Oxygen has 8 protons + 8 neutrons =
16 daltons
Radioisotopes (in blue) used in research:
HYDROGEN = 1 proton, H (= mass of 1
Dalton)
TRITIUM = 1 proton + 2 neutrons, a -emitter,
3H
CARBON-12 = 6 protons + 6 neutrons
CARBON-14 = 6 protons + 8 neutrons, a emitter,
decays to 14N
PHOSPHORUS-32 and SULPHUR-35 are
also used
These and other low energy beta emitters
are used for tracing labeled molecules.
Radioisotope-labeled reactants were
used to show the where the C, H and O
go in photosynthesis.
You do not have to memorize this figure at this time.
But you will later in the topic of photosynthesis
For human cells which of the
following is the most dangerous element?
Why?
A. 32 Phosphorus
B. Oxygen
C. 14 Carbon
D. 3 Hydrogen
E. All are equally dangerous.
Molecular weight:
Sometimes proteins are identified simply
by their MW (e.g. P53 is a protein of
53,000 daltons)
Molarity:
MOLECULAR WEIGHT AND MOLARITY
MgSO4. 7H2O, molecular weight = 246.7g
1 mole = 246.7g
1 mole in total of 1 L H2O = 1 Molar solution, abbrev. 1 M
1 mole in total of 10L H2O = 0.1M solution
24.67g in 100ml of H2O = 1M solution
1mmole (mM) solution, use 246.7 mg (= 0.2467g) in 1 L
NaCl, molecular weight = 58.44g
to make a 1mM NaCl solution (0.001M), with a total
volume of 100 ml:
[58.44mg/L] or 5.844mg NaCl/100ml,
The concentration of sodium chloride
(MW = 58.4 g/mole) is 150 millimolar
(mM) in blood. How would you make a
100 ml solution at that molarity?
A.Add 150 grams of NaCl to 100 ml of water
then stir to dissolve.
B.To 58.4 grams of NaCl add water to 100
ml and stir to dissolve.
C.Add 0.876 grams (=58.4 times 0.15 times
0.1) of NaCl to 100 ml and stir to dissolve.
D.To 0.876 grams of NaCl water add to total
100 ml and stir to dissolve.
Answer ____ is correct.
B. Biochemical bonds
The ______________________of electrons in the outer
shell determines chemical properties of the elements.
Covalent bonds result from sharing valence
electrons. The atoms get a lower therefore more
stable energy state.
B. Biochemical bonds
The number and distribution of electrons in the outer shell
determines chemical properties of the elements.
Covalent bonds result from sharing valence
electrons. The atoms get a lower therefore more
stable energy state.
Covalent bonds can have
variable degrees of polarity.
Figure 2.13
Five Types of Biochemical Bonds
Type
Strength
Van der Waals 0.6-1 kcal/mole
H bond
1.5-3
Ionic bond
3-7
Covalent bond 60-100
Double covalent 150
Interaction
Location
complementary
non-polar
electrostatic
areas
H attraction to mainly hydroelectronegative atom philic areas
electrostatic
same
sharing valence
electrons
same
everywhere
You need to know this table and where the
bonds are in a protein (next slide)
same
A type of covalent bond (peptide bond) links amino
acids of proteins (shown as a green ribbon)
Many H bonds on the protein surface(not shown)
greatly stabilize protein structure and make it soluble.
Note from the previous slide that H bonds and
ionic bonds would be most sensitive (i.e. broken)
by changes in the water solution.
All of the bonds are additive in contributing to
maintaining the structure of the molecule.
Main points about bonds: The number
and kind of molecular bonds formed
determines the __________________ of
the molecule and its interactions with other
cellular molecules.
For a protein, ______ determines function.
Main points about bonds: The number and
kind of molecular bonds formed determines
the shape and stability of the molecule and
its interactions with other cellular
molecules.
For a protein, shape determines function.
C. The special chemistry of water
Water is a polar molecule.
Therefore its a good solvent for ________
__________molecules.
H bonding is abundant between water and
dissolved hydrophilic molecules, (and between
and among polymeric molecules like proteins).
C. The special chemistry of water
Water is a polar molecule.
Therefore its a good solvent for charged
hydrophilic molecules.
H bonding is abundant between water and
dissolved hydrophilic molecules, (and between
and among polymeric molecules like proteins).
Cells are ~ 70 % water and therefore the
solution of 30 % hydrocarbon molecules in
a cell is very concentrated (see next
slide).
Note density of molecules
and relative sizes of
molecules.
You do not
have to know
these
molecules and
their
arrangement.
From Dobson, C. Nature Dec.
2004 Chemical Space in Biology.
Water is a
polar
molecule
The H
bonds make
it easy for
salts to
dissociate
into ions.
Water makes a _______ _____ around dissolved
proteins and other hydrophilic molecules.
Fig. 3.8
Water makes a hydration shell around dissolved
proteins and other hydrophilic molecules.
Fig. 3.8
Nonpolar molecules with nonpolar C-H
bonds (e.g, greases and oils)
are ___________ (cannot form many H
bonds) and water separates from them.
Certain types (phospholipids) can form thin
layers (the membranes).
Figure 5.14
Nonpolar molecules with nonpolar C-H
bonds (e.g, greases and oils)
are hydrophobic (cannot form many H
bonds) and water separates from them.
Certain types (phospholipids) can form thin
layers (the membranes).
Figure 5.14
H2O is in equilibrium with H+ + OH- which
dissociate from it.
The pH scale
(pH is negative log of H+ concentration)
pH = -log [H+]
Neutral soln, H+ is 10-7 M at 250 = pH of 7.0 = 0.0000001M
2 times higher
pH of 6.7 = 0.0000002M
5 times higher
pH of 6.3 = 0.0000005M
10 times higher
pH of 6.0 = 0.000001M
1,000,000 times higher pH of 1.0 = 0.1M
You do not
have to
memorize
this scale.
The pH of soil near the polar cap region of
Mars was determined to be 8.3. How much
more basic is this versus pH 7?
A. 1.3 times more basic.
B. 8.3 times more basic.
C. 13 times more basic.
D. Almost 20 times more basic.
Answer ___ is correct.
Acids, bases and buffers
Strong acids: HCL dissociates almost
completely into H+ and Cl- in water.
HCl
H+ + ClWeaker acids are in equilibrium and not fully
dissociated as in the example for acetic acid.
CH3COOH
CH3COO- + H+
Buffer like carbonic acid reversibly releases
H2CO3 (H+ donor acid)
HCO3 - +
H+
Blood pH is 7.4 and maintained in a narrow
range. Just 0.4 pH lower or higher is lethal
because the bonds of proteins are disrupted and
they lose shape.What bonds in a protein would
be least broken by increasing or decreasing pH
0.4 unit?
A. Peptide bonds.
B. Ionic bonds.
C. Hydrogen bonds.
D. Van der Waals forces.
Suggestion for use of the study guides:
Make a definition of the term and use the
term in a sentence to make what you
consider to be the most important point or
points which include the term.
Then if in doubt ask me or Jameel in the
review session or compare your answers
to those of fellow students.
Purification of a particular protein from all the other
molecules in a cell is a difficult but needed process in
order to get enough of the protein to effectively study
it. The objective is to find a series of steps which will
take advantage of the particular biophysical
properties of one protein type to separate it from the
lipids, sugars, nucleic acid and other proteins in a cell
(a cell extract). Which of the following do you think
would work? Why?
1. Add an acid to the extract.
2. Add a more hydrophobic solution (e.g. alcohol) to
the aqueous cell extract.
Study guide 1 terms to know:
enantiomer (optical isomer)
macromolecule
polymer
anabolism
catabolism
compartment
prokaryotic cell
eukaryotic cell
adenosine triphosphate
Central Dogma
Atomic weight (mass)
radioisotope
Molecular weight
molarity
Valence electrons
covalent bonds
polar covalent bond
nonpolar covalent bond
ionic bonds
hydrogen bonds
Van der Waals interaction (bond)
hydration shell
Study guide 1 terms continued:
Hydrophilic
Hydrophobic
pH
acid
Base
See also the study guide 1 in ANGEL for problems.
Hydrocarbons and Functional Groups
Ch. 4 pp.58-66
The closer one looks
at these
performances of
matter in living
organisms, the more
impressive the show
becomes. Max
Delbrck in A
Physicist Looks at
Biology
I. The four properties of carbon which
contribute to molecular diversity
1. Carbon has a valence of four and can
form four stable covalent bonds.
-with four single bonds a tetrahedron
shaped molecule forms
- double bonds result in a planar shape
Double covalent C=C bonds result in a planar
shape.
2. Chains of differing length of linked C can
easily form.
Shapes of Molecules
Ethane
Methane
You do not have to know the structures.
Ethene
Is this
molecule
polar or
nonpolar?
Does this
molecule
have two
versions,
right and lefthanded?
3. Three types of isomers may be formed: (a)
structural, (b) geometric and (c) enantiomers.
How do these two isomers differ?
(b) Geometric isomers:
How do these two isomers differ?
(c ) Enantiomers (mirror image nonsuperimposable molecules); the asymmetric
carbon is bonded to four different atoms
How do these two isomers differ?
4. Branching and ring formation of linked C can
form.
You need to be able to recognize this structural formula.
The tetrahedron shape, ability to form
chains or rings, the isomeric forms allows
great diversity of hydrocarbon
macromolecule shape.
If C had not been used for life here on Earth
which other element would best have fit in its
place?
II. Seven main functional groups
on hydrocarbon molecules
For small molecules these groups determine
the chemistry possible for that molecule.
For macromolecules these do that and play a
large role in the shape and stability,
hydrophilic or hydrophobic character and
therefore the function of a molecule.
Most molecules have two or more different types
of the seven.
Main point: A macromolecules surface with its
functional groups determines its interactions,
and therefore its function, with other molecules.
1. What complementary partner molecules;
2. what parts (domains);
3. the strengths of the fit
are all determined by the surface chemistry.
Because much of the chemistry occurs in aqueous
solution hydrogen bonds are critically important for
molecular structure and function.
Figure 4.1 in text lists the 7 types
You need to know the chemical structure, an
example and functional properties of all seven.
Alcohols
And
sugars
Polar (i.e.
aids
Solubility)
Note: a hydroxyl group is NOT a hydroxide
ion
Carbonyl
group as a
middle C
is a ketone
but if on
an end C
is an
aldehyde
Creates
molecular
Diversity in
structure
Usually at
cell pH is
in anion (charge)
form and
acidifies
solution
Usually at cell
pH is in cation
form (+ charge)
and deacidifies
solution.
Can be used in
H bonding.
Often used in
creating
disulfide
linkages
between parts
of one protein
or between
two proteins
(aids in
making
structure)
Role in energy
storage in
molecules (e.g.
ATP)
Main role in
protein
structure and
therefore
function.
A very important regulatory mechanism in cell
biology concerns phosphate as a functional
group.
Phosphorylation (addition) by enzymes called
kinases or dephosphorylation (removal) by
enzymes called phosphatases of phosphate
groups on proteins is a major mechanism for
regulating that proteins activity. See next
slide.
You do not have to
know this reaction
series at this time.
The only one of
the seven that
is nonpolar and
decreases
solubility.
Can be added
by methylases
or removed by
demethylases.
A comparison of functional groups on female
(estradiol) and male (testosterone) steroid sex
hormones
Main point is that small changes in functional groups
can have large effects.
Estradiol and testosterone
You should recognize these multi-ring compounds as steroids but do not
have to know the full structure nor the differences between the two
steroids.
Note how the shape of the two steroids look even
less alike when the 3D model is shown.
Only the estradiol will fit into the estrogen receptor
(of females) and only the testosterone will into the
testosterone receptor (of males)
Study guide 2 terms to know:
Tetrahedron
hydrocarbon
Structural isomer
Geometric isomer
Cis isomer
Trans isomer
Enantiomer
Asymmetric carbon
Functional group
Hydroxyl
Carbonyl
Carboxyl
Amino
Sulfhydryl
Phosphate
Phosphorylation
Dephosphorylation
Methyl group
Figure 4.2x Shapes of Molecules
Ethane
Methane
Ethene
Figure 4.4x Hydrocarbons: molecular models
Butane
Isobutane
Hexane
Cyclohexane
Estradiol and testosterone
- Cells are ~70 % water and therefore there is a ~30 %
solution of macromolecules (very concentrated)
96 % of the elements are C, O, H, and N and most of the
rest is P, S, N and Ca, with traces of others
These are not necessarily a set of the most abundant inorganic
elements of the earth (e.g. C is 600 fold enriched meaning it
must have had useful properties for life)
- Compounds are combinations of elements:
To get the MW add up the elements masses in the right
ratio.