Syllabus - Lone Star College System

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Dec 3, 2012 (4 years and 4 months ago)

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Page
1



COURSE SYLLABUS

for

BITC 1402

Biotechnology Laboratory Methods and
Techniques

CATALOGUE DESCRIPTIO
N

Laboratory operations, management, equipment, instrumentation, quality control techniques, and
safety procedures.
Includes laboratory practice in sampling and storage of bio
-
molecules using
pH meters, mixing buffers, performing measurements, preparing solutions, and performing
separatory techniques.


CREDITS
:

4


PREREQUISITES

BITC 1211; CHEM 1405 or 1411; MATH 1314;
or instructor’s approval; ENGL 0305 or 0316
AND ENGL 0307 or 0326, OR higher level course (ENGL 1301), OR placement by testing.


ADA STATEMENT

The Lone Star College System

is dedicated to providing the least restrictive learning environment for all
students. The college district promotes equity in academic access through the implementation of reasonable
accommodations as required by the Vocational Rehabilitation Act of 197
3, Title V, Section 504 and the
Americans with Disabilities Act of 1990 (ADA) which will enable students with disabilities to participate in
and benefit from all post
-
secondary educational programs and activities. If you require reasonable
accommodations
because of a physical, mental, or learning disability, please notify the instructor of this
course within the first 2 weeks of the term.

Students with disabilities who believe that they need accommodations in this course are encouraged to contact the
Disab
ility Services Office at 936
-
273
-
7239; located in Building E, Office 103H as soon as possible to better ensure
that such accommodations are implemented in a timely fashion.


COURSE OUTCOMES


1.

Students will demonstrate the preparation

of various solutions
, including buffers, to make
dilutions and to accurately measure and transfer solutions volumetrically.

2.

Students use the appropriate S.I. units in laboratory calculations and solve problems
involving conversions between unit expressions.

3.

Students
will collect data using a pH meter. Students will adjust the pH of various
solutions and determine the capacity of various buffer solutions by titration.

4.

Students will use a spectrophotometer to perform simple spectroscopy experiments.

5.

Students will

demonstrate a mastery of the fundamentals of low pressure column
chromatography, including ion exchange and gel filtration, by performing

separations of
mixtures utilizing low pressure column chromatography.

6.

Students will employ safe laboratory techniqu
es and demonstrate prudent laboratory
behavior.


Page
2


INSTRUCTOR

Larry Loomis
-
Price, Ph.D.

OFFICE
Bldg B Office 22
0
D


Email

lloomisprice@LoneStar.edu


Phone

Work

936
-
273
-
70
76

Fax

936
-
273
-
7362



http://faculty.lonestar.edu/lloomisprice/
OFFICE HOURS

Posted on my door, on my website and handed out in class. Other times are available by appointment.
If I am not in my office during the posted time, please check the biotechnology lab, room
B229

PROPOSED CALENDAR

See attached. The calendar is
subject to c
hange
. I will give you as much notice as possible when
changes occur or are anticipated.


SEMESTER / LOCATION
/ TIME

Spring 20
1
2

B233 (Lecture)

B229 (Lab)


8:30 to 11:30 Tue and Thurs





REQUIRED TEXTS


Basic Laboratory
Calculations Biotechnology.
Lisa A. Seidman
, 200
8
.
ISBN: 0
-
13
-
223810
-
1


Basic Laboratory Methods for Biotechnology.

Lisa A. Seidman, Cynthia J Moore,
Second Edition, 2009.
NOTE: The second edition is substantially different from the first
edition. ISBN: 0
-
321
-
57014
-
6


Lab Notebook


Scientific Notebook Co.


All are available in
the
college bookstore.

REQUIRED EQUIPMENT

Scientific Calculator

Safety Glasses or Goggles


these must be worn in the laboratory.

A Lab Coat
-

Local purchase (approx. $25)

Latex
or Nitrile
Gloves
-

May be ava
ilable in college bookstore or locally

Waterproof Finepoint Marker blue or black ink.





3

ATTENDANCE EXPECTATI
ONS



Attendance is mandatory. If you are unable to attend a class occasionally, you are responsible for
the material presented during that session
as well as any activity. Please be sure to jot down the
phone numbers of one or two classmates for assistance in these instances.



Because of the difficulty of making up complex laboratories spanning multiple class periods, it is
very difficult to make up
missed laboratories. However, if documentation of extenuating
circumstances is present, the student will be responsible for inquiring about alternate arrangements
that may be possible.



Participation in class discussions and activities is crucial since thi
s course emphasizes the
development of technical skills, communication skills, the ability to work responsibly in a group,
and the honing of critical thinking skills.



You will be graded for this participation (
5

points
per week
)
. By definition, you must
be in class
to
receive credit
.
You will receive a score of 0 for any activity that takes place during an unexcused
absence
.

If you have 3 unexcused absences
from the laboratory
you will be
barred

from the
lab

for the safety of the other students.

This mean
s you will fail the course.


NO LONGER ATTENDING CLASS DOES
NOT

CONSTITUTE WITHDRAWAL FROM THIS
CLASS, NOR DOES A STUDENT’S NOTIFICATION TO THE INSTRUCTOR THAT THE
STUDENT WISHES TO BE DROPPED. FAILURE OF A STUDENT TO FILL OUT A
“SCHEDULE CHANGE FORM” TO O
FFICIALLY DROP THIS CLASS MAY RESULT IN A
GRADE OF “F.”

THE LAST DAY TO DROP THIS CLASS AND RECEIVE “W” IS

APRIL
10
,
20
10
,
BY NOON
.
AFTER THIS DATE, NO WITHDRAWALS WILL BE ISSUED.



ADDITIONAL NOTES

Professional behavior is required in all lectures and laboratories in this course. This includes
observation of safety procedures, courtesy to your peers, respect for the equipment and reagents and
cooperation in group projects. Students will be expected
to maintain appropriate decorum in the
classroom and may be dropped from the class for unruly or disruptive behavior.


Often research is a cooperative effort. Many of our experiments will be performed of groups of two
(rarely three). It is important that
each individual contribute to completing the experiment. Data
obtained as a group is shared but each person in the group is required to record raw data in their lab
notebook and to write up their own lab report in their own words and to produce their own g
raphs,
tables etc. Individual grades will reflect individual effort.


COUNSELING

Counseling is available for academic, career, and personal matters. Contact either:


Terry Albores

Office: B2
00S

Phone: (936) 273
-
7074, or


Amy Roberson

Office: B
120H

Phone: (936) 273
-
7039





4

EVALUATION

Three Lecture Tests:

100 points each

= 300 points

Comprehensive Final:

200 points


= 200 points

1
0

Participation Grades

5 points



=
50

points


5 Assignments

10



=
50

points

Lab Grades:


Notebook prep

10 points (x
1
4
)


= 1
4
0 points


Long reports

60 points (x
2
)


= 1
2
0 points


Writing grades

(2
0

pts and
40

pts)

=
60

points


Short reports

4
0 points (x
4
)


=
16
0 points


Practicals
/Skills

60

pts



=
60

points

Approximate Total





1140

points


EVALUATION (CONT)

Letter
grade:


A


100
-
90%; B


89
-
80%; C


79
-
70%; D


69
-
60%; F


Below 60%


Note that a grade of “C” or higher is required in BITC courses in order to obtain the AAS
degree or ATC certificate.


MAKE
-
UP EXAMS WILL BE GIVEN ONLY FOR AUTHORIZED ABSENSES; WRITTEN
PROOF (FROM A DOCTOR, FOR EXAMPLE) WILL BE REQUIRED.

THERE WILL BE NO MAKE
-
UP LABS.

Late assignments will lose 10% credit. After one week, a late assignment may be turned in only with
permission of the instructor for 1/2 credit.

Test Corrections: For th
e hour
-
exams (but not the Final exam), an opportunity to make test corrections
will be given for partial credit. Details will be given in class.


Extra credit
: No other extra credit will be offered or allowed.

PROFESSIONAL ETHICS

I regard high profession
al standards as one of the most important lessons you can take from this class.
My expectation for this class is that each of you will act in a responsible and ethical manner. Please
take a look at the sections in our course catalog on Academic Integrity

and Appeals (p.
7
1
) for details
on your responsibilities as a student.


You as individuals are responsible for completing all assignments in this course. You may consult
with other members of the class on homework, laboratories, projects and exam
corrections

(NOT the
exams themselves), but I expect each of you to do your own work.
If you work with another student,
please note whom you worked with on the assignment.


The laboratory reports
& papers
are the responsibility of each student. The bac
kground, in particular,
requires that you do background research. Such research must be reported
IN YOUR OWN WORDS

and
REFERENCED APPROPRIATELY
. Inappropriate use of other work or citation will result in a
grade of “0” for the exercise. There will be
no

warnings
.


If there is reason to believe you are not meeting those standards, you may expect appropriate
disciplinary actions to be taken, as described in the catalog.


5

LABORATORY

LABORATORY SAFETY



Review the safety procedures described in chapter 2 of th
e Laboratory Manual (Seidman and
Moore). You are responsible for learning and observing safety procedures. You must sign and
date a Biotech Laboratory Safety Agreement before you will be allowed to work in the lab. Be
sure that you check the MSDS (copy in

the lab) before using any chemical.



All students must wear a
lab coat and safety goggles or glasses in the laboratory at all times
,
unless told to do otherwise. If you fail to bring your lab coat and goggles (glasses), you will be
asked to leave the lab
.
Lab

coats
may be stored

in the lab. You may bring a combination lock
to put on one drawer in the lab to store goggles, gloves etc.



Lone Star College System (LSCS) is committed to maintaining the safety of the students,
faculty, staff, and guests while visiting any of our campuses. See
http://www.lonestar.edu/oem

for details. Register at
http://www.lonestar.edu/12803.htm

to receive emergency notifications.
In the event of an emergency, contact LSCS Police at (281) 290
-
591 or X5911.


THE LABORATORY NOTEBOOK

Our partner companies have emphasize
d repeatedly how important good notebook skills are for their
employees. To help you meet their standards we will follow a specific set of guidelines for keeping
lab notebooks.

1)

The notebook must be bound, with numbered pages.

2)

You will write only in ink.
You will not remove pages, erase or deface any entries. You can
make changes by using a single strikeout
like this

and dating the change.

3)

Pages 1
-
3 will be reserved for the Table of Contents.

4)

Before you walk into the lab for an experiment, the following m
ust be in your notebook:

a.

Title of the experiment

b.

Description of the experiment (3
-
5 sentences per day)

c.

HYPOTHESIS for the experiment.
You may need to be creative, but you can come up
with one!

d.

Flow diagram for the experiment, including anticipated time.

e.

All necessary calculations.

f.

Blanks to fill in data to be acquired.

g.

Do not rewrite the protocol.
Refer to the written protocol, as necessary.

h.

NOTE any changes given to you about the laboratory, written or otherwise.

i.

Date

j.

Entry in the Table of Contents.

k.

Answ
er any questions or perform any calculations given to you with the protocol

l.

YOU WILL BE GRADED IMMEDIATELY ON THESE ENTRIES
.

5)

Modifications and safety notices from the instructor will be written down in the notebook.

6)

All data, all observations, changes, p
roblems etc will be made directly in the notebook.
It is not
necessary to rewrite the protocol.

It's only necessary to describe variations from the protocol.
Include details about all reagents, materials and equipment used.

7)

If you are observed writing any

of this information anywhere but your notebook it will cost you
points on the spot.




6

8)

At the end of EVERY LAB PERIOD, you AND the instructor will sign and date every new
page of data entry. Missing the signing will cost you credit.

9)

Leave
one

page blank at the end of each experiment. Your lab write
-
up and answers to
assigned questions will be written up SEPARATELY (see below) and turned in for grading.
The returned, graded write
-
up will be incorporated into the notebook by stapling in onto t
hat
blank page.


LAB REPORTS



Lab reports are separate from your lab notebook. Lab reports are due one week after each lab is
completed.
All lab reports must be generated using a computer and Microsoft Excel and
Microsoft Word; handwritten reports are not a
cceptable.
Computers are available in the
science/math area of the ELC (Extended Learning Center).

Computers are used by all
biotechnology laboratories and companies want people who know how to use them.



There will be TWO laboratory report formats used th
is semester: full format and
worksheet/answers.

WORKSHEET/ANSWERS

You will download the appropriate answer sheet from the course website and fill in the blanks,
including some short answers. No regrades are allowed on these reports.

FULL
LAB REPORT



FULL LAB REPORTS
must be produced using a word
-
processing program such as
Microsoft
Word
. All graphs should be produced using
Microsoft Excel

and pasted into the Word document or
otherwise incorporated into your report (see below)
.



Proofread your lab repor
t before you turn it in. Make the necessary corrections. Well
-
written
reports will get better grades than poorly written ones. If you have trouble writing scientific
English for any reason, consult with me early in the semester and we will arrange for ap
propriate
help.



These reports will be graded in detail, including a writing grade. You will be allowed the
opportunity to correct these reports and turn them in to obtain a better grade.


Lab Report Format:

o

Introduction:

Describe the problem and what the lab report is about in one to two pages. Give
some background
--

one sentence is not enough. You will be expected to include one or more
references. Include a copy of your
hypothesis

(from your notebook) with every lab
.

o

Materials and Methods:

Include a detailed protocol. Refer to the protocol that you have followed,
and describe all changes.

o

Results:

This is an important section. Raw data does NOT go here. Try to use your data to tell a
story. Use a computer to make
all graphs. Be sure that each figure has an explanatory legend. Use
complete sentences.

o

Conclusions:

This is the place for your interpretations and your conclusions. Please
do not

summarize your experiment here. Describe the results and account for accura
cy, precision, errors
and mistakes.
State whether your hypothesis was proven or no
t. What could you do to make this a
better lab or continue with the result you obtained? Answer all questions posed.

o

Raw Data and Calculations:
Put these at the end. Normall
y these would not be part of a lab
report, but they will allow me to help you trap errors if there are any in your write
-
up. Put the data
into useful tables.



7

LAB CLEAN
-
UP

You

are responsible for cleaning up after yourself. No one likes
“that person”

who
leaves a mess! The
biotechnology program is designed to help give you the training to prepare you for the workplace. I
will assume that you are not ready if you do not keep your area clean and neat or if you leave your
glassware in the sink for someone el
se to do.


Student
s

will be assigned to check various important areas of the lab each class period to make sure
that the areas are completely cleaned and ready for the next class.


Proper maintenance of individual and group areas is a GRADED ACTIVITY in t
his course.


GLASSWARE CLEANING I
NSTRUCTIONS

You

are responsible for cleaning and rinsing any glassware with distilled water
that you use before you leave the lab.


1.

Rinse all glassware 3
-
4 times with tap water before placing the glassware in the detergent.
These rinses will serve to remove chemicals so they are not transferred to the detergent and
then potentially to someone’s hands.


2.

Wash all glassware with dete
rgent. Use a brush to help to remove chemicals.


3.

Immediately rinse each piece of glassware 4
-
5 times with very warm water. Detergent can
cause problems if it is left to dry on the glassware.


4.

Then, rinse the glassware with
distilled water
.


5.

La
stly, place the glassware on the peg board to drain or, if the peg board is full, place on clean
paper towels, upside down (unless it is unstable), next to the sink so the glassware can drain.


LAB BENCH

Clean up all of the area that you worked in. Wipe u
p any spills as they occur. Be sure that you have
left equipment in the proper state i.e., pH electrodes should be placed in pH 7 buffer, set for standby
and the air hole closed.


Balances:

Clean any spills around the balance immediately.



Chemicals:

Re
place caps on chemical bottles immediately and wash and rinse any spatulas that you
may have used. Dispose of the weighing boats.


Pasteur pipets:

These are disposable. They are to be disposed of in the
Glass Only

box.
Do not

put
Pasteur pipets in the sink

to be washed. They break too easily and someone will receive a cut or
puncture.


Glass Only Box : Do not
put paper in these boxes.



Biohazardous materials : Place in one of the biohazard bags.




8

KEEP TRACK OF YOUR C
URRENT GRADE

Assignment

Your

Score

Possible

Your

Total

Possible

Total

Percent

Grade















































































































































































































































































































9

TENTATIVE CLASS SCHE
DULE


Assignments in Seidman and Moore, 2
nd

edition (SM)*, Seidman (Seid), or the on
-
line lab
book

LECTURE TOPIC

LECTURE
READING

LAB TOPIC

LAB
BOOK

Week 1


January 17, 19

1) Introduction to a safe workplace.


2) Working Safely in the Laboratory:
clothing, gloves & eye protection



3) Safety Video: Practicing Safe Science
HHMI

4) Glassware Washing

Hazards.

5)
The Measurement of
Mass and Volume

6) Introduction to Accuracy and Precision

7)
Math quiz, part 1

math basics:
exponents and scientific notation; the
metric system


SM:

Ch 9
-
12;

533
-
537

Ch 13; 19,

20


Seid: 1, 3

Laboratory orientation: labwa
re,
equipment,



reagents, care and maintenance.
Handling


chemicals and solutions. Glass, paper
biological waste disposal.


Glassware cleaning.

Care and use of laboratory balances.


Use of volumetric glassware.


Using a Pasteur pipette
.


Using a Mohr
pipette

Skills check:
10 mL Mohr pipet.


Skills check:
Use of the balances







p 23

p 28


Week 2

January
24, 26

1) Things you need to know before you
start the first lab:

2) Solution basics; making a solution at a
given concentration

3)
Math:
solution/dilution, part 1

4
)
Water in the lab

5) Theory of acids and bases

pH, pH meters and pH electrodes

6
)
Acids & Bases Problem Set

http://www.biology.arizona.edu/bioch
emis
try/problem_sets/ph/ph.html






SM:

Ch 28 (I
-
III)

Ch 26

Ch 22


Seid: 2, 11,
15

Calibration and use of the pH meter
and electrode.

Observe individual
calibration of pH meter.

Lab exercise:
Making up solutions
of strong acids, strong bases, weak
acids
and weak bases

Skills check:
Use of the pH meter

Demonstration

on the use of the
program, Microsoft Excel for making
graphs and inserting them in a
Microsoft Word document.

Extended Learning Center:
Math &
Science Computers

Using the directions on pages 9
-
11,
complete Lab Assignment 1
.


P 35






Week 3


January 31, February 2

1
) Buffer basics

2) Mathematics Review: significant
figures, decimals, scientific notation.

3) Significant figures tutorial
s:

http://science.widener.edu/svb/tutorial/sigf
igures.html

and
http://www.lon
-
capa.org/~mmp/applist/sigfig/sig.htm

)

4
)
M
ath Quiz: solution/dilution part 2:


Review dilutions



SM:

Ch 27


Seid 4, 12,
13


Lab Exercise:
Preparation of
phosphate buffer stock solutions.

29

Introduction to
Micropipettes.

Practice with instructor observation.

Skills check:
micropipettors


Extended Learning Center:

Graphing, continued.

Lab Assignment 2






P
29



P 43


10

Week 4


February
7, 9



EXAM 1: Feb
9



1)
Spectrophotometry

2
) Before you start the third lab:

Basics of using a visible
spectrophotometer

3
)
Mathematics review:
Descriptions of
d
ata:
p
opulations, samples, variables and
measurements of central tendency and
dispersion (mean, variance, standard
deviation, coefficient of variation and
normal distribution).


SM:

Ch 23, 25


Seid 16,
18, 19




Lab Exercise:
Micropipette

Calibration Check.

Short write
-
up, with statistics


How to write up your data and
appropriate conclusions

Observe individual setup & use of
spectrophotometer.

Lab Exercise:

Making a simple dye
solution and visible


spectroscopy.


P
45





P 50

Week 5


February
14, 16

1) Protein purification overview, part 1

2)
Mathematics: review dilutions;
applications of Beer’s La
w


SM:

Ch 29, 33


Lab exercise:

Pipetting and
Micropipetting check using the
spectrophotometer

First major
lab report

(spectroscop
y labs)
.


P 61


Week 6


February
21, 23

1) Protein purification overview, part 2

2)
Mathematics: making a purification
table; math quiz: graphing using
logarithmic data




Seid: 25


Finish up labs (catch
-
up day)



P 72

P 74

Week 7




February
28,
March 1

1) The Centrifuge.

2) The Centrifuge Video: Basic
Centrifugation Techniques.

3) Safety Video: Centrifugation Hazards
HHMI

4)
Mathematics: Centrifuge
calculations and use of a nomogram;
theory of dialysis



Molarity calculator

of Laboratory
SolutionMolarity calculator



SM:

CH 31, 32


Seid: 5


Overview of Protein Purification

Lab Exercise:

Preparation of
saturated ammonium sulfate

Lab Exercise:

Precipitation of rabbit
serum


Lab Exercise:

Dialysis

Lab Exercise:

General assay
methods;
Detecti
on of protein peak
by UV spectroscopy.

Writing a scientific hypothesis.

Writing methods and materials
sections.


P 67

P 69


P70

P 72

Week 8


March
6, 8

1) Structure of Proteins
; primary structure
(amino acids) and secondary;
amino acid
problem set

2)
Mathematics:
Weight per
volume vs
Molarity, Percents

solutions and
, Parts.

3
) Molarity calculator
http://chem.salve.edu/chemistry/molarity.
htm
1)

4) Video: Column Chromatography.


Handout


Lab Ex
ercise:
. Setting up a DEAE
anion

exchange cellulose column

Lab Exercise:

Purification of rabbit
immunoglobulin by ion exchange
chromatography.


Short Lab Write
-
up.


P 74

March
13, 15



Spring Break






11

Week 9


March
20, 22



EXAM 2: MARCH 22



1)
Structure of Proteins
; tertiary and
quaternary structure and function

2)
Mathematics: pH/pKa of amino acids
and zwitterions; the isoelectric point

3) Mathematics: 3
-
D structure
visualization and manipulation

4)
Large Molecule Problem Set
http://www.biology.arizona.edu/biochemis
try/problem_sets/large_molecules/large_m
olecules_problems.html


Handout


Continued.



Week 10


March
27, 29

1)
Immunochemistry

2) Use of animals in the laboratory;
production of monoclonal/polyclonal sera

3)
Mathematics: serial dilutions;
graphing ELISA data


SM:

Ch 17, 24



Lab Exercise:
ELISA in the
identification of proteins.

Short

lab report





Hand
-
out

Week 11

April 3, 5

1) Upstream processing; preparation of
cells and fermentation


2)
Videos: (Fractionating a Cell
)


3) Mathematics: fermentation yields


SM:

Ch 30


Seid: 17


Lab Exercise

Analysis of IgG
fractio
ns

using gel electrophoresis.

Second Major
Lab Report

(Purification of IgG).


P 83

Week 12

April
10, 12

1)
Biotechnology and the Regulation of
Medical and Food Products

2) Enzyme kinetics; enzyme reactions


SM:

Ch 3, 4, 5

Lab Exercise:
Lysozyme: Enzymatic
activity and crystallization of
lysozyme.

Short

lab report

(lysozyme).


P 93

Week 13

April
17, 19

1)
Introduction to Product Quality
Systems

2)
Mathematics: dosage of
pharmaceuticals

SM:

Ch 6, 8


Seid: 9


Continue




Week 14

April
24, 26



EXAM 3: APRIL 22



1) Documentation : The Foundation of
Quality

2) Quality Systems in the Laboratory


3) Safety Video, OSHA Safety Video,
Safety in the Research Laboratory
(Radionuclide Hazards, Chemical
Hazards, Emergency Respons
e).


SM:

Ch 7



Lab Exercise:

Production of a
product under GMP Conditions.

Short
lab report (GMP)
.


Hand
-
outs

Week 15

May 1, 3

Catch
-
up.



Clean up and check out.


FINALS WEEK



May 8, 10

May 8, REVIEW; May 10,
FINAL
EXAM