BIOL/MBBE 402 Biochemistry Handbook - Make Mānoa...

Biochemistry 2016 (Fall) BIOL/MBBE 402

BIOL/MBBE 402

Biochemistry Handbook

Understanding the chemical complexity of life and disease….

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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.”

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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

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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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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.

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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.

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• 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!

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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

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(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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(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

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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


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


20 21 Lecture 13

22 23 Lecture 14


25 WEEK 6 2hr exam

26 Lecture 15

27 28 Exam I (L1-14) Start 7:30 am

29 30 Lecture 16

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October 2016

Sunday Monday 8:00-9:20 Tuesday Wednesday


WEEK 6


2 WEEK 7


4 5 Lecture 18

6 7 Lecture 19


9 WEEK 8


11

12 Lecture 21

13 14 Lecture 22

15

16 WEEK 9


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


30 WEEK 11

31 Lecture 29 Halloween

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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


6 WEEK 12


8 Election day (No Recitation)

9 Lecture 32

10 (Yes Recitation)

11 Veterans Day


13 WEEK 13 (Normal Recitation)


15

16 Lecture 34

17 18 Lecture 35

19 OLD EXAMS III RELEASE

20 WEEK 14


22 (Yes Recitation)

23 Lecture 37

24 Thanksgiving Day (No Recitation)

25 Non-Instructional Day


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


WEEK 15

1 2 Lecture 39

3

4 WEEK 16


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


14 Biochemistry Final = 3hr, evening exam 5:30 to 8:30 pm



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

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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

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Biochemistry 2016 BIOL/MBBE 402

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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

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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

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BIOL/MBBE 402 Biochemistry Handbook - Make Mānoa...

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