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Biochemistry Discussion
BI 421/527/
Fall 2019
Jose Medrano, PhD
Biochemistry Lab Coordinator
Whitty Group Postdoc Associate Lecturer
Discussion sections (1 h 45 m) C1: M 12:20 – 2:05 pm, KCB-107C2: T 3:30 – 5:15 pm, PSY-B51C6: W 2:30 – 4:15 pm, SCI-117C3: R 9:00 – 10:45 am, SOC-B
Laboratory sections (4 h) B1: W 8:00 am (Chris and Raavi)B2: W 1:25 pm (Dr. Grossman and Ndidi)B3: W 6:30 pm (Hannah and Dr. Grossman)B4: R 8:00 am (Mike and Maggie)B8: F 6:30 pm (Raavi and Hannah)B9: M 2:30 pm (Ndidi and Mike)BA: T 8:00 am (Maggie and Chris) All labs are held in SCI 162
Office hours and contact info Mondays 3:30 – 5:30 pm, LSE 1004Thursdays 12:00 – 2:00 pm, LSE 1004(and by appointment)[email protected]
Biochemistry Discussion
Discussion will provide helpful notes to complete lab experimentsand
lab write-ups
for each chapter.
Quizzes
will be given at the end of every discussion. Discussion
attendance
is mandatory.
A lab comportment grade is assigned mid-way through thesemester (not counted) and at the end of the semester (
final
comportment grade
Lab grade is composed of:
Lab grade component
Percentage
Notebook write‐ups
Discussion quizzes
Discussion attendance
Final lab comportment
Final lab exam
Lab syllabus
Prerequisites •^
Must have earned a “C” of higher in Organic Chemistry II Questions, concerns, differences in opinion •^
Resolve it with your lab TFs first
-^
Try e-mailing both TFs in the same e-mail
-^
I will try to answer e-mails within 24 hr (
[email protected]
•^
Don’t forget to check lab blackboard site Required materials •^
Textbook:−
Biochemistry Lab Manual
, Tolan & Medrano, 4th Edition (BU Bookstore)
•^
Lab Materials:−
Safety eyewear −^
A lab coat −^
A bound, carbon-copy style notebook (carbon-copy pages are tearable) −^
Black or blue pens (
NO pencils or white-out!
−^
Scientific calculator
Lab syllabus (cont.)
Lab safety Dress appropriately
•^
Closed-toed shoes, long pants, t-shirt, long hair tied back, and a lab coat
-^
Safety eyewear worn
at all times
No food, drink, or consumables of any kind allowed
NOR
visible in lab
No cosmeticsLab gloves go in regular trash cans unless told otherwiseAll used plastics, sharps, and solid waste go in designated containers (read the signs)All hazardous chemicals disposed of appropriately (TFs will advise each week)Arrive to lab on time with tool kits
before the hour
. Do not arrive late!
Repeat violations will result in dismissal for the day and willnegatively impact your comportment grade
Lab syllabus (cont.)
Pre-laboratory write-up
: Complete this every week
before
lab
A complete pre-lab write-up entry for full credit includes two parts:I. Part 1 (completed before lab, turned in at beginning of lab)•^
Name
,^ Date
, and
Title
•^
Introduction
: three to four sentences about the purpose of your experiments and
your objectives for the day
-^
Procedure
and
flowcharts
: write down
in your own words
( not verbatim from
the manual
) a protocol for the assays and experiments you will accomplish for the
day. Check the notebook section of the manual for required flowcharts II. Part 2 (completed before lab, collect data during lab, submitted at end of lab)•^
Prepopulated tables
for data collection and
prompts
for recording observations
•^
Equations
and
calculations
prepared for in-lab “plug and chug”
•^
Start Part 2 on a new page
; these carbon copies are turned in at end of lab
Meet with your lab partner(s) beforehand to better organize your time in lab Preparation is key in this course!
Lab syllabus (cont.)
Attendance and Absences Discussion and lab attendance is mandatory Making up lab work •^
Anticipated absences (e.g. jury duty, BU athletics, interviews)−
Notify lab TF ASAP! Give no less than a week of notice( *must be cleared by TFs and Jose
•^
Sudden emergencies (e.g. family death, hospitalization, accident)−
Requires bona fide documentation (e.g. funeral program, physician’snotice, police report)
Quizzes No make-up quizzes for discussion are available past the discussion date(unless sudden emergency with proper documentation) If you anticipate missing a discussion, you must contact Jose more thana week in advance to take a different quiz
Academic Conduct Violations in Academic Conduct •^
Photocopying from lab manual or discussion slides
-^
Copying from lab partner, current students, or previous students (any part ofthe notebook)
-^
Copying verbatim from lab manual (introduction and lab procedures)
1st offense = zero for assignment; referral to the Dean2nd offense = failure of course; referral to the Dean Students are free to talk about data and experiments
,^
but
required to work independently on post-lab write-ups
Lab syllabus (cont.)
Your laboratory manual
In each chapter: Introduction
•^
Concepts, assays, and experiments in the chapter are explained
Problems
•^
While these problems are for your own benefit and will not be graded,you are highly encouraged to do these on your own. These practiceproblems will help with calculations for the
Notebook
section.
References
•^
A list of references from the
Introduction
section
Experimental Procedures
•^
A step-by-step explanation on how to perform the experiments
Notebook
•^
Use this section for completing your pre-lab and post-lab write-ups
Set-up and Materials
•^
A list of reagents, materials, and equipment you will need
Appendix
•^
Answers to the
Problems
section as well as other useful information to
help you complete your notebook write-ups
Your laboratory manual (NEW!)
Addition of Student Friendly Features (SFFs) – page 4 of Introduction Chapter-^
Learning Points
- reinforcing important key concepts -^
Hazardous Reagent
- informing students of hazardous
chemicals and reagents used in particular procedures
-^
Time Saver
- suggestions on how to better organize
certain tasks to maximize efficiency in lab
- calling attention to particular procedures
or equipment that requires special care
-^
Ask the Instructor
- pointing out when TF assistance is
needed/required
-^
Tips & Tricks
- suggestions on how to perform a
particular procedure while reducing difficulty and hassle
-^
Online Video^ -
Links to Youtube videos by scanning the corresponding QR codes
-^
iPhones – “QR reader” (free in the App Store)
-^
Android – “QR code scanner” (free in the Play Store, some ads)
Your laboratory notebook
It is your responsibility to keep and maintain professionalnotebook throughout the course! -^
Black or blue pen
only
-^
Neatly strike through mistakes
-^
No white-out, no pencils
Your laboratory notebook (cont.)
For a complete lab write-up, each week you must have: Pre-lab write-up
(submitted in lab)
•^
Title, date, introduction, procedure and any necessary tables andflowcharts
Data Collection
(submitted in lab)
•^
Show filled data tables and experiment recordings
-^
You are responsible to having all of your data in your notebook. Graphsand charts based off of missing data will receive no credit and begrounds for academic misconduct.
Notebook Section
(post-lab write-up)
•^
Complete each prompt and exercise, including
Questions
, from the
Notebook
section for each week in the lab manual
Conclusions
(post-lab write-up)
•^
One or two sentences about the results of your experiments + completeanalysis
Sample Calculations
(post-lab write-up)
•^
Show a sample calculation for each different type of mathematicalmanipulation
-^
Credit will not be given to values with no sample calculations and aregrounds for academic misconduct.
Chapter 1: Photometric Methods forProtein Determination Objectives •^
Learn two colorimetric methods to measure protein concentration
-^
Generate a standard curve and observe effect of interfering substances
-^
Observe absorbance spectra of different macromolecules
Procedures •^
Use Lowry Method and Dye-Binding assay to determine protein concentration
-^
Use UV/Vis spectrophotometer to detect nucleic acids and amino acids
Protein assays
Colorimetric methods (destructive) Lowry Method
•^
Sensitive to differences in
time
(stay consistent when adding reagents)
•^
Method is a combination of
two reactions
•^
Biuret Reagent: alkaline solution of copper ions−
Turn pink/purple when exposed to protein backbone
•^
Cupric Reagent−
Dependent upon aromatic amino acids
Dye-Binding (Bradford) Assay
•^
Utilizes the dye Coomassie Brilliant Blue G250, absorbs light at 465 nm
-^
Upon binding proteins,dye absorbs light at 595 nm
-^
Some reagents act as interferingsubstances and affect absorbance−
You will test the effects of someinterfering substances
http://www.eiroforum.org/media/photo_galleries/embl/embl-03l.jpg
[Protein]
Protein assays (cont.)
Ultraviolet Absorbance (non-destructive) Proteins absorb light at 280 nm, primarily because of tryptophan residues,and to a lesser extent, phenylalanine and tyrosineContribution of light absorption at wavelength 280 nm: It is difficult to create a standard curve for a heterogeneous sampleof protein since amino acid composition varies among proteins
