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Biochemistry 2016 (Fall) BIOL/MBBE 402
BIOL/MBBE 402
Biochemistry Handbook
Understanding the chemical complexity of life and disease….
Page 1 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
BIOL 402 Biochemistry
CRN 70354 MWF 0800-0920a BIOMD B103 Tutorial: Tues. 0800-0850a BIOMD B103 CRN 76975 MWF 0800-0920a BIOMD B103 Tutorial: Thur. 0300-0350p BIOMD T208
MBBE 402 Biochemistry CRN 71673 MWF 0800-0920a BIOMD B103 Tutorial: Tues. 0800-0850a BIOMD B103 CRN 75866 MWF 0800-0920a BIOMD B103 Tutorial: Thur. 0300-0350p BIOMD T208
Course Supervisor/Instructor: Dr. Jon-Paul Bingham, E-mail: [email protected]
Teaching Assistances: Mr. Ray Zhang <[email protected]> Mr. Erik Saksa <[email protected]> Mr. Nicholas Sinclair <[email protected]>
Official Office Hours*
Mon. Tue. Wed. Thu. Fri.
Dr. Bingham Ag. Sc. Rm 415L
10:30 -11:30 am 10:30 -11:30 am 10:30 -11:30 am
Mr. Ray Zhang Gilmore Rm 108
10:20-11:20 am 10:20-11:20 am 10:20-11:20 am
Mr. Erik Saksa Gilmore Rm 108
10:00-11:00 am 4:00-5:00 pm
Mr. Nicholas Sinclair Gilmore Rm 108
2:00-3:00 pm 4:00-5:00 pm 10:00-11:00 am 2:00-3:00 pm
If you are unable to locate Dr. Bingham, go to Rm 210 St. Johns (Dr. Bingham’s Laboratory)
Unofficial Hours: Dr. Bingham is usually accessible outside “Official Office Hours” on a
‘catch me if you can’ basis for course related matters.
But requires an appointment, arranged via e-mail, in advance, if you are seeking guidance into graduate courses/research.
“The most helpful piece of advice I can give to enable you to succeed in this course, is to follow the format closely and develop a basic study
routine in doing the homework, reading the book and undertaking the Homework.
You will have to work hard in doing this.”
Page 2 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
Biochemistry:
Overview: This course will provide a foundational core of Biochemistry, with a medical orientation. This course is designed to specifically enhance student understanding in the related courses. Students will be required to demonstrate comprehension of materials and well as illustrate their application in solving biochemical related questions and problems. Format: Students will be provided with a weekly course outline, providing clear indication to the topics covered, the concepts required to be mastered. The course will utilize materials provided by Lehninger ‘Principles of Biochemistry, 5th Edition’, as too the teaching and learning resources associated with this text. Students will be guided to questions/problems and will be provided homework throughout the course.
______________________________________________ Areas that will be covered range from:
• Basic concepts in understanding Biochemistry; • Properties of Amino acids, Peptides and Proteins; • Protein structure and function; • 3D Dimensional structure of proteins; • Enzyme kinetics; • Carbohydrate and Glycobiology; • Carbohydrate Pathologies; • Nucleotide and Nucleic acids; • Lipids and Lipid diseases; • Biochemistry of membranes and Biosignaling, and; • Bioenergetics; • Glycolysis • Metabolic regulation • The Citric Acid Cycle • Fatty Acid Catabolism • Urea Cycle • Oxidative Phosphorylation • Photophosphorylation • Photosynthesis
Page 3 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
Course Grading Breakdown: Grades are a reflection of what students know and how students apply that knowledge, a bell curve is not. Therefore I will NOT undertake the practice of curving marks.
Grading components:
No. Type Points allotted 2* 80 min. Examinations @ 80
marks
160
1 3 hr. Final Examination 200 marks
200
10 Homework @ 10 100 Attendance (8%) 40
TOTAL 500
*NOTE: Students may select two (2) examinations marks out of the FIRST three (3) examinations + the final Examination to count towards ONLY their final grade. Total Maximum = 500 points No extra credit is given
Comment: Each little grade soon adds to a big final grade – Do your best to do the best everytime! Grading: I believe that I am a fair grader. I try to award points, not take them off.
“Your class taught me a really valuable lesson: when you get an opportunity, you take it, no matter what. You pretty much give us every opportunity to get an A+ (1.) you give us hw which you grade!!! 2.) you give us practice exams weeks before the tests 3.) you drop the lowest exam grade 4.) you hold review sessions where you go over problems 5.) you go over exams with each individual student……. Your grade in the class is completely dependent on how much effort the student puts in. Opportunities to succeed in life don't come often, so you need to take them.” Biochemistry Student (Fall) 2011.
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Biochemistry 2016 (Fall) BIOL/MBBE 402
Grading Chart: Total Maximum = 500 points allowable
Grade points/500 A
≥475 95.0 -100.0
≥ 95%
A- 474 – 450 94.8-90.0
90%
B+
449 – 425 89.8-85.0
85%
B
424 – 400 84.8- 80.0
80%
B- 399 – 375 79.9 -75.0
75%
C+
374 – 350 74.8-70.0
70%
C
349 – 325 69.8- 65.0
65%
C- 324 – 300 64.8-60.0
60%
D+
299 – 275 59.8 -55.0
55%
D
274 – 250 54.8-50.0
50%
F
<249 ≤ 49%
Student Learning Outcomes for the Biochemistry Course:
1. Know and apply scientific terminology; 2. Know applications of certain biochemical technologies and their limitations; 3. Undertake problems from textbook/provided in class and from internet resources: 4. Participate in problem classes/tutorials; 5. Apply this knowledge to the basic understanding and application of appropriate best practices in biochemical based investigations; 6. Develop biochemical problem-solving skills; 7. Develop strong study skills; 8. Develop collegial practices in groups study; 9. Understand the scientific method and design of experiments to test hypotheses and as such experience the process of discovery. 10. Explore the relationship between Biochemistry and society.
Page 5 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
This course is not solely about getting grades – it’s about you getting the skills to survive in the graduate or working world beyond UH.
In the real world there are no second chances, without a cost. Plagiarism: Cheating or plagiarism takes many forms and is regarded as a very serious offence in the scientific community. Acts of cheating or plagiarism will NOT be tolerated and will be dealt with in full, as described in the procedures outlined by Academic Disciplinary Board at University of Hawai’i.
It is natural that students will be tempted to discuss homework, examination questions and share ideas. BUT remember this:
• That I will be the ONLY ONE grading the Homework/Examinations
As soon to be UH graduates and professionals – I am sure that acts of plagiarism or cheating will not happen. Yet in the real world people lose reputation, dignity and employment over it.
Plagiarism is a crime and will be dealt with accordingly
This course is a 400 level, 4 credit course and thus must be treated accordingly. There is no easy way, short cuts etc. in taking this course.
There is no extra credit provided – your efforts reflect your grades directly.
Ideally you should be reading everyday doing your homework little by little, you
may have to read specific chapters 2-3 times!
Review the lecture notes time and time again.
This is not ‘kiddie college’ – this course is the first step for many professional careers.
Page 6 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
• Course Attendance: Attendance is compulsory for all classes, as outlined in the Course Calendar.
Exemptions on medical grounds be accompanied with a medical certificate specifically mustindicating the dates of illness date of visitation. AND Other exemptions can be provided at the discretion of the Course Supervisor. However, notice is required by e-mail in advance, usually 5 working days at minimum.
If you have a and reason you have nothing to fear. valid legitimate
Attendance will be taken: It is the responsibility of the student to sign the attendance sheet – THIS COUNT TOWARDS THE FINAL GRADE DOES
Attempt to falsify signatures on attendance sheets will result in course expulsion of BOTH parties.
In the real world if you do not show up to work, you get the sack – learn now about commitment and punctuality. I do not want to have to shut the doors at 3 min past, locking out the late comers, so be on time and be prepared!
Access to homework will be provided via Laulima to students who are present at lectures. ALL An attempt to hand in unofficial homework will result in recording . zero for the homework
We control student access to this site based on attendance. Non attending students will have access ‘denied’ and will be unable to undertake the required work or gain lecture notes – UNTIL THEY SEE ME PERSONALLY WITH DOCUMENTATION ….. or IF YOU DID NOT COME TO CLASS AND YOU HAVE NO LEIGITMATE REASON YOU WILL BE ASKED TO JUSTIFY WHY YOU SHOULD CONTINUE WITH THIS COURSE IN WRITING BY PROVIDING A LETTER ADDRESSED TO MYSELF AND THE CHAIR OF THE DEPT.
If by chance you do miss a lecture and are unable to hand in the homework for some reason, valid provide me e-mail notification BEFORE Monday 5:00pm and then see me as soon as possible. This is again for and reasons ONLY. valid legitimate Sorry “the dog chewed up my homework” or “my computer blew up” is not a valid or legitimate reason. I do not teach for my education – I teach for yours – YOU SHOULD GET EVERY LITTLE BIT YOU PAY FOR!
Page 7 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
To obtain Lecture slides: Here students will be required to enter via Laulima (MY UH Portal), here we control your access to slides and provide important announcements and directions regarding web-based quizzes. If your class attendance is lacking, your access to this information will be denied. Lecture slides will be post usually on the Saturday the week before, in whole week files – this includes the homework and crossword. My suggestion is print off a ‘note’ version of the lectures so you can add your comments as the lecture is presented.
We do not provide handouts of lecture notes.
To help organize yourself I would suggest: • Purchasing a large ring bind folder(s) • Separate the sections into weeks • Divide lecture notes, homework and web-based quizzes • Add a section for past examinations (we will provide these closer to the date) • Keep it organized and it will be easier to review Also note that the textbook is now available in loose-leaf form for this specific reason – so you do not have to carrier the large textbook
Page 8 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
(A) Homework: Students will be provided:
• Multiple choice questions • Short answer questions • Calculation problems/questions
Homework will be provided, together with lecture notes, on the Saturday prior (see Course Calendar). Homework will submitted by placing in the box provided outside St. John’s Rm 210, on the Monday as specified in the course calendar, by 5:00pm Please make sure Homework bares your name and assigned biochemistry STUDENT NO. (this is NOT your UH No.) – printed all text clearly.
The correct way to prepare for the homework AHEAD OF TIME, is to understand the lecture content, read the requested chapters, and ask questions during class.
Suggestion: Keep up with the reading
20 % of final grade
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Biochemistry 2016 (Fall) BIOL/MBBE 402
(B) Examinations: Three (3) examinations (@ ~80 min.) + one (1) accumulative final (@ ~3 hr) – see Course Calendar. A Total of four (4) examinations
Examinations will contain:
• Multiple choice questions • Short answer questions • Calculation problems/questions
These will reflect the lecture notes, Homework questions in the chapters indicated by the Course Calendar. Students are required to undertake ALL four (4) examinations Students will be able select two (2) of their better examination grades from examinations 1-3 ONLY The final accumulative 3 hr examination is a compulsory component of the course
• Students who are unable to attend these examination times, MUST see me seven (7) days in advance or earlier to make arrangements for alternative testing dates.
• Students with sport/team commitments, who may be unable to attend these examinations- due
home away games, have your coaches notify me via e-mail seven (7) in advance or earlier, to make arrangements for alternative testing dates. NO NOTIFICATION, NO EXEMPTION
• If unable to attend examinations due to medical reasons – a medical certificate be MUST
presented – specifically indicating the dates of illness date of visitation AND
• If no notification is provided within the requested period prior to the scheduled examination, as indicated in the Course Calendar, the grade will be recorded as a ZERO
Suggestion: Keep up with the reading and homework
72 % of final grade
Page 10 of 19
August 29 Last day to drop courses/switch sections without "W" grade August 30 to October 21 In-Person Restricted Withdrawal Period (with "W" grade) August 31 Last day to register/add courses/change grading option
August 2016 Sunday Monday
8:00-9:20 Tuesday Wednesday 8:00-9:20 Thursday Friday
8:00-9:20 Saturday
1 2 3 4 5 6
7 8 9 10 11 12 13
14 15 16 17 18 19 Statehood Day
20
21 WEEK 1
22 First day of instruction Lecture 1
23 24 Lecture 2 Homework 1 provided
25 26 Lecture 3 27
28 WEEK 2
29 Lecture 4
30 31 Lecture 5 Homework 1 Due by 5pm
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September 9 Last day for to file application for graduation for Fall 2016
September 2016
Sunday Monday 8:00-9:20
Tuesday Wednesday
8:00-9:20 Thursday Friday 8:00-9:20 Saturday
WEEK 2 1 2 Lecture 6
3 Homework 2 provided
4 WEEK 3
5 Labor Day
6 7 Lecture 7
8 9 Lecture 8
10 Homework 3 provided
11 WEEK 4
12 Lecture 9 Homework 2 Due by 5pm
13 14 Lecture 10
15 16 Lecture 11
17 OLD EXAMS I RELEASE
18 WEEK 5
19 Lecture 12 Homework 3 Due by 5pm
20 21 Lecture 13
22 23 Lecture 14
24 Homework 4 provided
25 WEEK 6 2hr exam
26 Lecture 15
27 28 Exam I (L1-14) Start 7:30 am
29 30 Lecture 16
Page 12 of 19
October 2016
Sunday Monday 8:00-9:20 Tuesday Wednesday
8:00-9:20 Thursday Friday 8:00-9:20 Saturday
WEEK 6
1 Homework 5 provided
2 WEEK 7
3 Lecture 17 Homework 4 Due by 5pm
4 5 Lecture 18
6 7 Lecture 19
8 Homework 6 provided
9 WEEK 8
10 Lecture 20 Homework 5 Due by 5pm
11
12 Lecture 21
13 14 Lecture 22
15
16 WEEK 9
17 Lecture 23 Homework 6 Due by 5pm
18
19 Lecture 24
20 21 Lecture 25
22 OLD EXAMS II RELEASE
23 WEEK 10
24 Lecture 26
25
26 Lecture 27
27 28 Lecture 28
29 Homework 7 provided
30 WEEK 11
31 Lecture 29 Halloween
Page 13 of 19
November 2016 Sunday Monday
8:00-9:20 Tuesday Wednesday 8:00-9:20 Thursday Friday
8:00-9:20 Saturday
WEEK 11 2hr exam
1 2 Exam II (L15-28) Start 7:30 am
3 4 Lecture 30
5 Homework 8 provided
6 WEEK 12
7 Lecture 31 Homework 7 Due by 5pm
8 Election day (No Recitation)
9 Lecture 32
10 (Yes Recitation)
11 Veterans Day
12 Homework 9 provided
13 WEEK 13 (Normal Recitation)
14 Lecture 33 Homework 8 Due by 5pm
15
16 Lecture 34
17 18 Lecture 35
19 OLD EXAMS III RELEASE
20 WEEK 14
21 Lecture 36 Homework 9 Due by 5pm
22 (Yes Recitation)
23 Lecture 37
24 Thanksgiving Day (No Recitation)
25 Non-Instructional Day
26 Homework 10 provided
27 WEEK 15 2hr exam
28 Lecture 38
29 30Exam III (29-37) Start 7:30 am
November 8 Election day (no school) November 23 Last day for examinations before finals
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December 2016
Sunday Monday 8:00-9:20 Tuesday Wednesday
8:00-9:20 Thursday Friday 8:00-9:20 Saturday
WEEK 15
1 2 Lecture 39
3
4 WEEK 16
5 Lecture 40 Homework 10 Due by 5pm
6 7 Lecture 41
8 Last day of Fall 2015 instruction
9 Fall 2015 Study Days
10 Fall 2015 Study Days
11 Finals Week
12 Final Examinations
13 Final Examinations
14 Biochemistry Final = 3hr, evening exam 5:30 to 8:30 pm
15 Final Examinations
16 Final Examinations
17
18 19 20 21 22 23
24
25 Christmas
26 27 28 29 30 31
December 21 Fall 2016 grades available via MyUH opens in windows or STAR opens in windows
Page 15 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
Lecture HW -
Exa
min
atio
n I
Week 1 What is Biochemistry L1 –L2 1 2 Water L3
Week 2 pH L4 3 Amino acids L5 1
Week 3 Protein analysis and purification L6 4 5 Protein structure I L7
Protein structure II L8 2 Week 4 Protein structure III L9
Protein Function L10 Proteins/Ligands L11 3
Week 5 Enzymes I L12 6 Enzymes II L13 Enzymes III L14 4
Exa
min
atio
n II
Week 6 Carbohydrates and Glycobiology L15 7 8
Glycoconjugation L16
Week 7 Lipids I L17 9 10 Lipids II L18
Biological Membranes and Transport I
L19 5
Week 8 Biological Membranes and Transport II
L20 12
Biosignaling I L21 Biosignaling II L22 6
Week 9 Bioenergetics L23 13 14 Glycolysis L24
Gluconeogenesis L25 7 Week 10 Metabolism of Glycogen L26 15
Regulation of Glycolysis and Gluconeogenesis
L27
E
xam
inat
ion
III
Week 10 Citric Acid Cycle I L28 16 Week 11 Citric Acid Cycle II L29
Fat and Glycolysis Oxidation of fatty Acids
L30 8 17
Week 12 FA regulation Pathological FA diseases; Ketone bodies
L31 - L32 18 and 19
Amino acid Metabolism; Urea cycle
L33 9
Week 13 Oxidative phosphorylation
L34
ATP Synthesis L35 Photosynthesis L36 10
Week 14 Make-up lecture L37 Make-up lecture L38
Week 16 Class Review L39 Class Review L40
Accumulative Final Examination
Page 16 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
HINTS FOR EXAMINATIONS
Know your pathways and structures – these will be tested – AGAIN THEY WILL BE IN THE EXAMINATIONS - LEARN THEM EARLY AND EARN THEM WELL (see mud map)
Understand and know the inter linkage between these pathways and their regulation
Know your amino acids – chemical functions, properties, 1 and 3 letter codes
KNOW YOUR METHODS FOR BIOCHEMICAL ANALYSIS OF PROTEINS
Know concepts and how to interpret hydropathy plots
Know your fats – and how they are breakdown
Understand processes in biosignalling, GCPRs, phosphorylation, Kinases etc
Know the fat/production of ATP
Know your enzymology
LISTEN CAREFULY IN CLASS AND TAKE NOTE WHEN I START TO DO STUFF ON THE BLACK BOARD
Page 18 of 19
Biochemistry 2016 (Fall) BIOL/MBBE 402
Course Contract
I, ______________________________ (Print Student Name), have fully read and will comply with the items as presented in the proceeding pages (pages 1-19) of the ‘Biochemistry Handbook’.
I will comply with directions given, keep to the requirements of the Course Calendar, and perform the work that is expected of me as a student participating in the “Biochemistry Course, BIOL/MBEE 402” (Name of Course) Fall Session 2016 (Semester, Year).
I fully understand that this course is solely dependent on my participation and my efforts as an individual. The grades provided will solely reflect my abilities and understanding of course material.
I clearly understand that if I have difficulties with course material or content, that reasonable assistance will be made available, yet I understand I have to make these requests, using the correct procedures.
I understand that this course is for my educational development, and that as a professional I will conduct myself in a manner that so deems the term.
______________________________________ (Student Signature) ____________ Date
Page 19 of 19