111 BS Cells and Molecules
Spring 2011 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 3:30 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 night before).
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).
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)
DATE POINTS Exam 1 (W) Feb. 9 100 2 (W) March 2 100 3 (W) April 6 100 Final Exam (W) May 4 200 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 46 500 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 LS A133 will be used for the exams. Before the exam you will be told which room to go to.
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 Applications of this knowledge: ______________________________
BS 111 covers the areas in red which form a foundation for biological understanding at all other levels. Biological Discipline Population Biology Organismal Biology Physiology Developmental Biology Cell Biology Biochemistry Molecular Biology Level of Analysis 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
WARNING: The many new terms with specific meanings used in each lecture will add up quickly. 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, RNA, NADH). For new terms I will briefly use the full term, e.g. Adenosine triphosphate, but then for convenience I will use ATP.
Overview/Chemical Bonds Ch. 3 pp.46-47,50--56
"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
I. A Big Picture view of seven unifying principles in all cellular life
1. The rules of physics and chemistry govern life. 2. All cells use the same set of core hydrocarbon-based molecules in an aqueous solution. -~1000 molecules ____________________
When available only one enantimor 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 polymer (linear molecules made by linking simpler molecules (e.g. proteins are amino acid polymers).
Shown is one way the beads on a string model to depict a protein
3. A core of multi-step biochemical pathways of synthesis (_anabolism_________), use and breakdown (_catabolism_________) of molecules is similar in all cells. points The black
represent key biochemicals and the green arrows show reaction pathways interconnecting them in a yeast cell.
The catabolism of various food molecules
Main point: The core metabolic functions are interconnected by reaction pathways.
You do not have to memorize this figure.
4. All cells are bordered by a phospholipid membrane making possible a compartment of those core molecules of life.
4. Continued...Only two cell types exist.
_prokaryotic________ cell____:two border membranes, no nucleus, limited internal membranes. eukaryotic_cell_______ _ ___: single outer membrane but extensive internal membrane-bordered organelles, with a nucleus
Comparison of chemiosmosis in mitochondria and chloroplasts
Mitochondrion and chloroplast are example of organelle compartments.
Which is a potential question topic on an important point for the first exam? A. Recalling verbatim Feynman's opening quote about physics and chemistry. 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 an animal cell? This will be the second clicker question. A. B. C. D. E.
5. Adenosine triphosphate (ATP) is universally used as energy currency.
You do not have to know the ATP structure at this time.
6. All cells, and viruses, use polymers of nucleic acids for inheritable genetic information.
The central______ dogma______of information flow occurs in all cells.
DNA
RNA Protein
7. All cells must arise from a preexisting cell.
Both daughter cells get the necessary genetic and paragenetic (spatial, organizational) information plus a high energy state to maintain life.
Figure 1.7
Themes for understanding cellular life 1. Energy:
2. Matter:
3. Organization:
4. Information:
II. Short review of the chemical context of life.
If you need a longer review of background inorganic chemistry see Ch. 2 (optional reading). Here we will focus on: A. Elements. Molecular Weight. Molarity. B. Bonds. Five important types. C. Water. Special properties. D. Carbon. Uniqueness for life's molecules.
From CEM I 141 will assume you understand these terms: Element, isotope, atomic number, atomic weight, dalton, electron, orbital, Van der Waals forces, ionic bonds, covalent bonds, hydrogen bonds, polar bond, non-polar bond, electronegative, molecular weight, molarity, anion, cation, hydrophilic, hydrophobic, pH
I will briefly give biological examples of their use to refresh your memory.
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
CEM 141 topics continued:
Atomic number = protons = 11Na Atomic weight (mass) = protons and neutrons = 23Na Oxygen has 8 protons + 8 neutrons = 16 daltons
Radioisotopes (in blue) used in biomedical 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.
An example: radioisotope-labeled reactants were used to show 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
Can you determine the molecular weight of glucose C6H12O6 ? Atomic weights are C = 12, H =1, O = 16
The MW of an average size protein that has catabolic reaction with glucose is 50,000 daltons.
Sometimes proteins are identified simply by their MW (e.g. P53 is a protein of 53,000 daltons)
CEM 141: 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?
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.
Also, covalent bonds can have variable degrees of polarity, as in water.
Figure 2.13
Polarity creates the opportunity for H bonds, which are very important for structure.
Five Types of Biochemical Bonds
Type Strength Interaction Location
Van der Waals 0.6-1 kcal/mole H bond Ionic bond 1.5-3 3-7
complementary non-polar electrostatic areas H attraction to mainly hydroelectronegative atom philic areas electrostatic same sharing valence electrons same everywhere same
Covalent bond 60-100 Double covalent 150
You need to know this table and where the bonds are in a protein (next slide)
A type of covalent bond (peptide bond) links amino acids of a protein (here shown as a green ribbon model)
Many H bonds on the protein surface(not shown) greatly stabilize protein structure and make it soluble.
Other important points from the previous slide: _______ionic bonds__________would be most sensitive (i.e. broken) by changes in the water solution.
The bonds are additive in contributing to maintaining the structure of the molecule.
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
As mentioned water is a polar molecule. Therefore it's a good solvent for _hydrophilic __________molecules. H bonding is abundant between water and dissolved 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.
The H bonds make it easy for salts to dissociate into ions.
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 hydrophobic (cannot form many H bonds) and water separates from them. Certain types (phospholipids) can form thin layers (the membranes).
Figure 5.14
But water dissociates at a low rate to hydrogen H+ and OH hydroxide ions.
H2O is in equilibrium with H+ + OH- which dissociate from it.
CEM 141 :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 pH is on a log scale
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.
CEM 141: 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 and accepts H+ ions.
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?
Suggestion for use of the study guides: Make a definition of the term and then use the term in a sentence to make what you consider to be the most important point or points which include the term. If in doubt ask me or Jameel in the review session or compare your answers to those of fellow students.
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.