Biology 201

From atoms to genomes.

10 weeks

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Jeff Young, Plant Geneticistyoung@biol.wwu.edux3638Office: BI412

Office Hours

MTW: 3:00 - 4:00 PM…by appointment.

Arabidopsis thaliana

Genome-based, molecular study of plant physiology and

environmental responses.

Registration

• The class is full, folks are waiting to get in,• 52 student capacity,• Sign the roster today!

• Those still wanting to get into the class, sign up after class.

Lecture/Recitation Schedule

Lecture: MTWR, 2-3 PM, B234

Lab: R (9-12) or F, 1-4 PM, BI261

– laboratory is mandatory,– no lab this week.

TAs

• Graduate TA: ?

• Undergraduate TAs:

– Eric Olson,– Emily Spitzer,– Jeannie Gilbert.

Class Business

• Bulletin Board outside of BI261,

– Graded exams and quizzes,– etc.

• Lectures online,

– WWU Biology Home Page, Courses.

Biologyby Cambell, et al., Fifth edition.

Reading Assignments: • Unless amended in class, all reading assignments listed on the syllabus are required, • Additional reading assignments may be made,

• You will be responsible for ‘in class’ additions and changes made to the syllabus.

Lab Manual

• No lab this week.

• Buy your lab manual ASAP,– Thursday, 11 - 12, BI261,– Friday, 1 - 2, BI261,

Preferred

Success is Easy

• Do the reading assignments before class,– don’t neglect the figures,

• Attend lectures,

• Listen to the lectures, look at the examples,– don’t copy every word from the PP slides.

Evaluation of Coursework

Three hourly exams (100 points each) 300

Lecture Quizzes (10 points each) 50

– 6 quizzes, drop lowest score,– No Make-Up!

Laboratory grade 150

Final lecture exam 150 600

Extra Credit• e-mail me a synopsis of a

newspaper story concerning biology,

• 1 point each for up to 15 points (2.5% final grade),

• paper, date, byline, who, where, what and the significance,

• in English sentences,– not an automatic point, – must be well presented.

Golden Age of Biology

• The last decade has seen an unprecedented accumulation of biological knowledge,

• With new technologies, the pace is accelerating.

Human Genome Project

…Human Genome Project began in 1990,

– jointly funded by the National Institute of Health (NIH), and the Department of Energy (DOE),

– consortium of countries including USA, Japan, Great Britain and France have formed the Human Genome Organization (HUGO).

Genome Project Goals

• Identify the + 60,000 genes in human DNA,

• Determine the sequences of the + 3 billion chemical base pairs that make up human DNA.

Sequence Technologies

• human sequence is completed, requires polishing and annotation,

• many genomes have already been sequenced,– bacteria,– fly,– worm,– yeast,– plants (some done),

• collect sequence data from the rest of the planet.

Sequence Variation

• Develop technologies for rapid identification of DNA sequence variants,

– to identify genes for the roughly 4000 genetically determined diseases,

• A new priority for the HGP is examining regions of natural variation that occur among genomes,

– between individuals, – between groups of individuals (ethnic variations).

Functional Genomics

• Efficient interpretation of the functions of human genes and other DNA sequences,

– assigning function to sequence.

Comparative Genomics

• Obtain complete genomic sequences for many species,

– A first clue toward identifying and understanding the functions of human genes or other DNA regions is often obtained by studying their parallels in non-human genomes.

Bioinformatics and Computational Biology

• Improve current databases,

– integrate current databases, standardize nomenclature,

• Develop new databases and better tools for data generation, capture and comprehensive functional studies.

Ethical Legal and Social IssuesELSI

1. Privacy and fairness in the use and interpretation of genetic information.

2. The transfer of genetic knowledge from the research laboratory to clinical practices.

3. Issues of informed consent for participants in genetic research.

4. Public and professional education.

Biology 201

Goal: to understand the chemical principles that underlie biological processes,

– the structure and function of biological molecules,– the cellular basis for life,– energy acquisition and cellular metabolism,– storage, transfer and expression of genetic information,– evolution, a unifying view of nature,– BROAD SCIENCE PICTURE.

Elements

Of the ~90 naturally occurring elements, less than 30 arerequired to sustain life on earth.

Electron Configuration

...electron shells: probable energy levels for electrons in any given atom,

– electrons in the outer shell are termed valence electrons,

...atoms with room for more electrons in it’s outer shell may react with other atoms.

1st shell

2nd shell

3rd shell

1 shell

2 shells

3 shells

Chemical Bonds

Covalent Bonds Sharing of pairs of electrons

Ionic Bonds Attraction of opposite charges

Hydrogen Bonds Sharing of H atom

van der Waals Interaction of electron clouds

Strong

Weak

Covalent Bonds

…a chemical bond that arises from the sharing of electrons between two atoms. Usually a strong bond.

Hydrogen Gas (H2)

Hydrogen Atoms

Electrons attracted by eachothers protons.

Covalently bonded hydrogen molecule H2.

Methane (CH4)

Multiple Covalent Bonds

• Single bonds are formed when a pair of electrons are shared,

H H

• Double bonds are formed when two pair of electrons are shared,

H2C CH2

Unequal Sharing of Electrons

…electronegativity: some atoms hold electrons more tightly than do other atoms,

– oxygen,– nitrogen,

…polar covalent bonds: a covalent bond in which the bonding pair of electrons is unevenly shared.

Polar Molecules

is the symbol used to denote charge differences.

(-) delta negative, the electron rich end of the molecule.

(+) delta positive, the electron poor end of the molecule.

Hydrogen Bond

…a chemical bond formed from the attraction between a slight positive charge on a covalently bonded hydrogen atom and an electronegative atom, usually oxygen or nitrogen,

…weak bonds, but of great importance in biological molecules.

Hydrogen Bonds

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+

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+

Ionic Bonds

…a chemical bond resulting from the attraction between positively and negatively charged atoms. Usually a strong bond.

11Na 17Cl

…ion: charged atom,…cation: positively charged atom (missing e-),…anion: negatively charged atom (extra e-).

Ions and stuff...

…ionic compounds are called salts,

…some salts have unequal numbers of anions and cations,

– Mg Cl2, K3 PO4, etc.

…complex ions: groups of covalently bonded atoms that carry an electric charge,

– NH4+, SO2

2-, etc.

Van der Waals Interactions

…weak attractions between molecules, or parts of molecules brought about by localized charge fluctuations.

VDW (London Forces)

Polar and Nonpolar Molecules

…when electrons are shared equally in a covalent bond, the bond is nonpolar,

– substances with nonpolar bonds are hydrophobic,

…when electrons are shared unevenly in a covalent bond, the bond is polar,

– substances with polar bonds are hydrophilic.

Likes Attract, etc.

Hydrophillic attracts Hydrophillic

Hydrophobic attracts Hydrophobic

Hydrophobic repels Hydrophillic

For Tomorrow

• Read through pp. 46 as assigned in the syllabus.