Topics
to know for winter biochemistry final.
Jim Neitzel
Lab I room 1022
(360)867-6463
neitzelj{use that funny
at
sign}evergreen.edu
Lehninger Principles of Biochemistry, 4th edition
David L. Nelson & Michael M. Cox
W. H. Freeman
ISBN 0-7167-4339-6
The work this quarter will return to proteins and will cover: review of
protein chemistry and protein structure; experimenatl methods for
examining proteins; properties and mechanisms of enzymes; and protein
synthesis, localization and modification.
Fall Archive:
First 3 workshop keys now up!
Workshop 5 & 6 keys up.
Text
The basic textbook for the fall quarter is
The Molecular Biology
of the Cell, 4th edition. (MBOC).
Reading assignments for each week are listed below. In the winter
quarter we will add a biochemistry text, and we will continue to use
MBOC for molecular biology. There will be occasional additional
readings from web sites and scientific papers.
Evaluation Basis:
Attendance and participation in weekly
workshops.
Performance on exams and quizzes, both
in class and take-home. This includes the ability to succinctly explain
and to use evidence to support the correct answers and approaches.
Laboratory notebook and work.
Written assignments.
Advice on studying and using the
text:
Plan on reading each text section several times. I recommend an initial
reconnaissance; look at the section headings, introduction and summary,
and the figures. What are the major ideas? Why are these structures and
processes important to organisms? What organisms do they occur in? What
size and scale are we examining?
Figures and illustrations in learning this material are important in
several ways. Many models for biological processes have branched
paths with multiple connections. A figure can help show all of these
connections. Figures can also simplify complex subjects. Always attend
to the figures and pictures in any of our reading assignments.
A very powerful study technique is to make
your own figures, summary diagrams, and outlines. When I am
learning a new area or experimental method, I find I often must use
this method. In responses to workshop and exam questions, a well
labeled figure may be the optimal solution..
Part of the learning that will help you throughout the year is paying
attention to commonly used methods. When theories or important
generalizations are presented, what experimental evidence is provided
that supports these models or contradicts other explanations?
The vocabulary in this area is enormous. Try to identify key words by
their frequency of use in text, illustrations, and lectures. You may
find a biological dictionary helpful. Also, start to pay attention to
common Latin and Greek roots. Knowledge of these roots will help you
learn vocabulary and usually helps your spelling as well. An important
reason to learn the vocabulary is to allow clear communication. As one
of my now retired faculty mentors says "you want to able to talk about
biology without sounding like a clod." Equally important, do not use a
word in your responses or solutions that you do not understand.
Work with other students and the tutor. One of the most frequent
behaviors that lead to students struggling in this class is becoming
isolated from other students.
You may
always feel free to contact me when you have a problem. I will post
specific office hours once I have a feel for the weekly schedule.
However, I will always schedule meetings with students. My preferred
format is for you to send me an email with a suggested meeting time,
and I will usually quickly confirm this. Good times to talk to me are
after class just about any day, before class or at lunch break on days
I am not teaching, and many Wednesday and Friday afternoons.
Particularly on days when I am teaching , I like to have my lunch hour
as a quiet oasis. Emergencies only at this time!
Lab and Lab Notebook:
Always come to lab in proper, safe lab attire: closed toe shoes, long
pants, hair tied back, safety glasses. Lab coats are optional but nice.
Always bring your lab notebook, both on lab days and on any other
days where you may need to take data or do some thinking about your lab.
A lab notebook (separate for biology and chemistry) should have a
sturdy cover and paper, and a sewn sturdy binding-no spiral or loose
leaf. The typical composition books, often on sale for 50 cents or so
are fine. As we will use graphs and tables, you may find the quadrille
rules style helpful.
Syllabus:
Week 1: Friday October 1, 10:30-12:30 LH5 (
This week only-normally in Lab I
1037/1047)
& 1-3 workshop Lab I 1037/1047 Use same groups as in genetics
workshop
Lecture review of important
biology MBOC pp. 1-44 (very similar to genetics review)
chemistry pp 47-57 (much the same
as discussed in organic)
Major classes of biomolecules pp.
58-70
Some thermodynamics review
pp. 70-90
GOOD Review and Reference Tool: Panels 2-1 to 2-7 (pp.110-123 in
MBOC . Worth tabbing)
LAB: Genetics, use of microscope,
polytene chromosomes and chromosome structure (
see
Genetics page)
Workshop 1 Key (clarification on
4b added.)
Week 2: Monday October 4, lecture Protein chemistry and structure
review MBOC pp. 129-163; 168-174; 176-180
Friday October 8. workshop
LAB:
Introduction to microbiological techniques I
Workshop 2 Key
Week 3: Monday October 11, lecture Cell Membranes MBOC pp. 583-612
Friday October 15, workshop
LAB:
Introduction to microbiological techniques II
Workshop 3 Key
Week 4: Monday October 18, lecture MBOC pp. 615-656 (emphasize 615-636
first) Review relationship between free energy and equilibrium constant.
Friday October 22, workshop Takehome
exam given out, due following Friday.
Lab:
Drosophila
(Genetics)
Week 5: Monday October 25, lecture MBOC Continue work on membrane
transport
Friday October 29, workshop
LAB: Use of toxins to study phagocytosis in Tetrahymena
Organic
Chem Exam 1 Monday
Workshop 5 key
Week 6: Monday November 1 Begin coverage of cell signaling and membrane
receptors. MBOC Chap. 15
Friday November 5
LAB:
Drosophila
(Genetics)
Genetics
Exam 1
Workshop 6 Key
Week 7: Monday, November 6 Cellular Signaling continued; protein
kinases. MBOC Chapter 15
Friday November 12 Workshop on cell
signaling.
LAB: Yeast genetics and cell biology
Week 8: Monday, November 15 Cell cycle control and apoptosis. MBOC
Chapter 17.
Friday November 19 Workshop on cell
cycle.
LAB:
Drosophila
(Genetics)
Week 9: Monday, November 22 Noted schedule this week! Lecture
Monday: Cytoskeleton MBOC Chapter 16
TUESDAY November 23 Workshop 10:30-12:00 Sem. II C1107 on cytoskeleton
Genetics Lab report due this week
Organic Chem Exam 2 Monday
Week 10: Monday, November 29: Cytoskeleton and molecular motors. MBOC
Friday December 3: In class exam:
Cumulative, but emphasizing second half of the quarter. (Cell
transport-signaling to cytoskeleton.) Short answer, multiple choice,
reading comprehension.
Genetics
Exam 2
Evaluation Week: December 6-10
Useful Links:
Cell image collections and animations:
Last update: September 24, 2004
by JJN