PRINCIPLES OF BIOCHEMISTRY

Sections 001 and 002 [Honors]

 

BCH 451& BCH 451H --------- Summer Session II 2013Lecture: Mondays, Tuesdays, Wednesdays, Thursdays and Fridays, 9:50 - 11:20 {200 Park Shops}

 

Review Session:         #401 Mondays Wednesdays,  1:00-3:30        {128 Polk}

                                    #402 Tuesdays Thursdays, 1:00-3:30             {128 Polk}

 

Prerequisite: CH 233, Organic Chemistry II (May be taken concurrently with consent of instructor.)

 

Description:   An introduction to and a survey of the fundamental concepts of biochemistry, emphasizing the chemistry of living organisms, chemical structures and the interactions of biomolecules.

 

Instructor:     Dr. James A. Knopp, 128 Polk Hall {Undergraduate Coordinator} 515-5828

515-5683 {appointments}email:jaknopp@ncsu.edu

                                    office hours: times by appointment

 

Assistants:     Becky Breese (402), Raveena Chhabria (402), Grey Fortenbery (401), Ameer Ghodke (401)

 

Texts:             H. R. Horton, L. A. Moran, R. S. Ochs, J. D. Rawn, and, K. G. Scrimgeour PRINCIPLES OF BIOCHEMISTRY (Fifth Edition), Prentice Hall Publishers, 2005 (required) $144

 

J. A. Knopp, KNOPP’S KNOTES, (Fifth Edition), Kendall-Hunt, 2010 (required) (must be new and not used)

 

J. A. Knopp, BIOCHEMISTRY HINTS, @ Sir Speedy (required), ~$4

 

Other:            A “simple” calculator { +, -, *, /, log, 10x} {no graphing or memory}

 

Plus and Minus Grading Scale is based on total accumulated points:

 

            200                              169                              139                              109

                        > A+                           > B+                           > C+                           > D+

            190                              160                              130                              100

                        > A                             > B                              > C                              > D

            180                              150                              120                               90

                        > A-                            > B-                            > C-                            > D-

            170                              140                              110                               80

 

Course Web site: http://www4.ncsu.edu/~knopp/BCH451/index.html

 

Audit requirement: sign and turn in quizzes, exams and in-class exercises.

 

Credit only:   Accumulate at least 110 points during the semester.

 

Honors credit: You will be given a handout later which lists the specific requirements.

 

Grading:        There will be short quizzes given at the end of each problem session for a total of 9 quizzes. Each quiz will be worth the same maximum points. The highest 7 quizzes will be totaled and be considered equivalent to one exam. Your quiz total is capped at 32 points. Four exams will be given during the lecture time, each worth at least 32 points. There will be a 72 point final exam. The exam schedule is given below: There will be no make-up exams or quizzes. Any missed quiz or exam will be recorded as a zero. Your grade will be determined as follows ➔ First the lowest of the four exams plus the quiz total will be dropped. Then the remaining four scores will be added to your score on the final and placed against the grading scale. I reserve the option of awarding additional points for in class activities and/or exercises.

 

 

 

            Exam #1         Wednesday, July 10               Chapters 1, 2, 3, 4

 

            Exam #2         Thursday, July 18                  Chapters 5, 6, 7, 8

 

            Exam #3         Friday, July 26                       Chapters 9, 10, 19 [++]

 

            Exam #4         Friday, August 2                     Chapters 11, 12, 13, 14

 

            Final              Friday, August 6 @ 8 am       Chapters 1 - 14, 19 [++]

 

[++]

            20.6 : dideoxy sequencing

            21.8 : tRNA & rRNA processing

            21.9 : mRNA processing

            22.1 : code/codons

            22.2 : tRNA structure

            22.4 : ribosomes

            23.2 : cloning

            23.5 : libraries

            23.11 : PCR

 

While the dates of the exams are fixed, the exact material covered will be determined prior to each exam.

 

HONOR CODE:

 

            I will expect that you are aware of the honor code and agree to abide by it as stated in the Code of Student Conduct. Specifically, it is my understanding that writing or printing your name on your exams, quizzes, extra credit papers means that you have neither given or received unauthorized aid, even though there is no specific Honor Pledge printed on each. I will vigorously pursue any incident of academic misconduct! The presence of a cell phone on your person during an exam will be considered evidence of cheating. http://www.ncsu.edu/policies/student_services/student_discipline/POL11.35.1.php.

 

QUIZ AND EXAM MAKE-UP POLICY:

 

            If you miss a quiz for whatever reason, the grade of zero will be recorded with no make-up possible since the two problem sessions are covering different material and the quizzes will not be camparable. However, there are sufficient number of points to be gained with quizzes so that missing one or two quizzes will not jeopardize your ability to earn the full 32 possible points. If you miss an exam for whatever reason, it will be recorded as a grade of zero. Your quiz total will automatically replace that score. I realize that with the large number of students in this course, missing quizzes and exams is inevitable. The above stated policy will cover these cases. If there is a planned or extended absence which this policy cannot cover, I will expect to discuss this with you prior to the exam or quiz and work with you on a case by case basis.

            The following is the url for the university policy on absences both excused and unexcused: http://www.ncsu.edu/policies/academic_affairs/pols_regs/REG205.00.4.php

 

DISABILITY POLICY:

 

             Reasonable accommodations will be made for students with verifiable disabilities. In order to take advantage of available accommodations, students must register with Disability Services for Students at 1900 Student Health Center, Campus Box 7509, 515-7653. Http://www.ncsu.edu/equal_op/dss/ If you have any documented limitations or special requirements, please inform me at the beginning of the semester so that the appropriate adjustments can be made.

 

STUDENT OUTCOMES:

 

By the end of the semester, a student will be able to:

 

1.         Draw and recognize the structures of various biomolecules at a specified pH.

 

2.         Describe the actions of buffers and how pH affections biomolecular structure and function.

 

3.         Repeat and use the definitions of various biochemical terms.

 

4.         Describe the properties [structures and functions] of the four classes of biomolecules and how these various structures are involved with their biochemical cellular functions.

 

5.         List and describe the various interactions which stabilize biomolecular structures.

 

6.         Describe the structures of hemoglobin and myoglobin and how various molecules influence oxygen binding and the delivery of oxygen.

 

7.         List and identify enzymes according to their classification.

 

8.         Calculate and describe the kinetic parameters of enzymes and its reversible inhibition.

 

9.         Describe the various coenzymes and how they participate in enzyme mechanisms.

 

10.       Describe the factors which are involved with enzyme mechanisms and rate acceleration.

 

11.       Describe the various signal transduction pathways

 

12.       Describe the central dogma and relate this concept to specific biomolecules.

 

13.       Describe all enzymes, cofactors, substrate structures, product structures, and regulation of glycolysis, gluconeogenesis, TCA cycle, β oxidation, and oxidative phosphorylation.

 

 

 

 

 

 

 

QUIZZES:

 

The quizzes will be given at the end of review/problem session. Typically, they will be very short, one to three questions. These questions will be more of the memory type questions, such as structures, definitions, solving a mathematic problem or short answers. They are designed to reward those students who keep up with the material. They will normally cover the more immediate information from lectures, i.e. the past week of lectures. Your TA will not know what is on the quiz and will not specifically prepare you for it. You will be expected to complete a quiz within approximately 10 minutes. To prepare for these quizzes, I recommend that you review the past week's material and work on the appropriate sections in Knopp’s Knotes.

 

EXAMS:

 

The exams will be given in the lecture time at the second half of the period. They will consist of questions at several different levels of understanding and sophistication. Previous year's exams will be posted on the Web page. Of course, I will not repeat questions.

 

Approximately 25 - 30% of each and every exam will involve drawing structures from the list of memorizable structures. You must show all atoms including carbons and hydrogens. You must show all bonds. You must show the correct ionized species for the specified pH. The penalty for omission will increase during the course of the semester.

 

The rest of the exams will be short answers, multiple choice, problems and/or essay questions. Unfortunately, it is not possible to examine all of the information assigned for a particular exam and still be of a reasonable length. Therefore, some important concepts will not be tested. The questions will be designed to test the depth of your knowledge and understanding. Some questions will require thinking, analysis and synthesis of information. Other questions will test for detailed information or analysis. Each exam will contain at least one question from the assigned homework. It will be either exactly as written or modified slightly.

 

There is usually one extra credit puzzler question. This question will be very difficult. The answer will involve analysis and synthesis of information that you possess but in a way that you have not done before. Missing this question will not prejudice your grade in any fashion.

 

The answers will be graded exactly (picky), but with generous partial credits. Spelling does count! It will be important for you to be clear and concise in your answers. The graders cannot read minds. State the obvious first and then get clever. All grading errors must be cleared before the start of the next exam.

 

The preferred way to prepare is to review the hints sheets. If you understand each concept and can explain it to a member of your study group, you should do well. If you try to "guess" what will be on the exam or just memorize the answers to last year's exam, you will not do well.

 

FINAL:

 

The final will be comprehensive, covering the entire semester’s material. It is designed to be graded quickly. In contrast to the previous exams, you will be asked to name structures instead of drawing structures. There will be pages and pages of fill-in-the-blank questions. There will be some tough multiple choice. The best way to prepare for this final exam is to go through the hints sheets line by line with a study partner.

 

My goals for you in Biochemistry 451:

 

1)        To learn a vocabulary of definitions and structures:

 

Biochemistry is like a foreign language in that you need to memorize a basic set of definitions and structures. Without that common vocabulary, I will not be able to communicate during lecture. I have attempted to establish the minimum number of memorizable structures and have included them in the HINTS study guide. If you will spend 10 - 15 minutes every day drilling on structures, that should be sufficient. As stated above, at least 25% of every exam will be on structures.

 

2)        To learn the properties of the four major biochemical molecular groups:

 

All biomolecules fall into four major categories. Each category has its own set of unique properties and characteristics. To help you organize the large volume of information which will be presented, I will emphasize these four categories and their appropriate properties.

 

3)        To learn enzyme kinetics:

 

Almost all chemical reactions which occur within the cell are mediated by chemical catalysts - usually enzymes. Many diseases are a consequence of imbalance or mal-functioning of different enzymes. In order to better understand these reactions, a knowledge of kinetics is essential. A part of kinetics is an understanding of how the rates of catalyzed reactions are modified by inhibitors and changes in the protein structure itself. Another aspect is the understanding of the role that cofactors play in the enzyme mechanism.

 

4)        To learn metabolism (glycolysis and TCA cycle):

 

These chemical reactions which occur within the cell are organized in sequential fashion in that the product of one reaction becomes the reactant (substrate) of the next in the series. A sequence provides a pathway in which one biomolecule is converted into an entirely different one. The study of these pathways is metabolism. Knowledge of metabolism not only includes an understanding of the chemistry which occurs but also of the control of the rate of the entire pathway through key enzymes and compounds. I have chosen two pathways for emphasis: glycolysis and the citric acid cycle. The first was chosen because of its primitive and universal nature. The second was chosen because of its potential for high energy yield.

 

5)        To incorporate (integrate) knowledge concerning biochemistry and cell biology:

 

Without some framework, the information in Biochemistry can appear fragmented and encyclopedic. To avoid these problems, I have elected to focus upon the cell and its problems and with the understanding of Biochemistry to show how the cell solves its problems. It is my hope that this approach will help make sense out of what we will study this semester.

 

Prerequisites:

 

1)Knowledge of cell biology: I expect you to know some basics about cells and their organelles. This will be quickly reviewed during the first lecture.

 

2)Knowledge of solution properties and pH: I expect you to remember basic chemical properties of solutions and have a working knowledge of pH, pKa and ionization and the appropriate calculations. This will be quickly reviewed in the second lecture.

 

            3)        Knowledge of organic structures and reactions:

 

                        a.         Oxidation and reduction, both organic and inorganic

 

                        b.         Resonance stabilization, aromatic structures

 

                        c.         Stereoisomers, stereo chemistry, optical activity

 

                        d.         Nucleophilic and electrophilic organic reaction mechanisms

 

                        e.         Chemical reactivities and characteristics of the following classes of organic compounds: Know the structures of the compounds given in the parentheses as their trivial or common names.

 

alcohols (methanol, ethanol, 2-propanol, benzyl alcohol)

 

phenols (phenol, p-nitrophenol)

 

ethers (dimethyl ether, diethyl ether)

 

ketones (acetone)

 

aldehydes (formaldehyde, acetaldehyde, benzaldehyde)

 

carboxylic acids (formic acid, acetic acid, propionic acid, butyric acid, benzoic acid)

 

anhydrides (acetic anhydride, acetyl phosphate, pyrophosphate)

 

amines (methyl amine, ethyl amine, butyl amine, pyridine, pyrimidine, purine, aniline, guanidine HCl == guanidium chloride)

 

amides and anilides (acetamide, acetanilide, urea)

 

mercaptans/thiols (ethyl mercaptan, 2-mercaptoethanol)

 

                        f.         Chemical reactivities and properties of chemical functional groups

 

alcohols, aldehydes, ketones, carboxylic acids, amines, phosphates, thiols/sulfhydrals, esters, ethers, amides, anhydrides, hemi-acetals, acetals

 

 

 

 

 

 

 

 

 

 

 

 

 

What you can expect from me:

 

1.         I will start and end class on time. In addition, I will provide a short break during class.

 

2.         I will answer as many questions as I can during lecture and all questions addressed to me during review sessions. I will encourage questions.

 

3.         I will answer all electronic questions within one working day.

 

4.         I will be available for consultations outside of the classrooms by appointment.

 

5.         I will grade as quickly as possible. In class exams will be returned within two class periods. Quizzes will normally be returned at the next review session.

 

6.         I will grade as fairly as possible and will re-grade any question submitted prior to the next exam/quiz.

 

7.         I shall endeavor to present the material as accurately and clearly as I am able. I will use many examples to illustrate the major points. I will emphasize the understanding of basic concepts

 

8.         I shall endeavor to structure the review sessions so as to be useful to you.

 

9.         I have minimized the amount of memorization and will emphasize learning concepts.

 

10.       I will do what I can to prevent cheating and will vigorously pursue any incidents that may occur.

 

What I expect from you:

 

1.         You will attend each lecture and review session. You will arrive on time and not leave until lecture or review session is finished.

 

2.         You will return any quiz/exam for re-grading prior to the next quiz/exam.

 

3.         You will inform me if you have trouble hearing lectures or being recognized with a question.

 

4.         You will become a member of a study group.

 

5.         You will go through your flash cards every day.

 

6.         You will read the text prior to attending lecture.

 

7.         You will bring questions to the review session and actively participate in them.

 

8.         You will work through the assigned homework questions in Knopp’s Knotes.

 

9.         You will spend at least six hours every week {2 hours/hour lecture} studying biochemistry.

 

10.       You will learn all of the information and concepts given in the hint sheets.

 

11.       You will turn off your cell phone and/or beeper during class and review sessions.

 

A Final Word

 

            Biochemistry 451 is a very difficult and time consuming course. The students who succeed are the ones who pursue consistent and efficient studying. The problem sessions are our way of providing peer tutoring to you. These sessions are for your benefit. You are expected to bring your questions and/or confusions. You are also expected to take an active part. These are not more lectures. The teaching assistants who are in charge of these sessions are dedicated and caring people. They can not do your job for you!

 

            I feel that you have an excellent set of notes -- your textbook. My lectures are designed to explain the textbook to you and help you sort out the information that is presented there. Part of this is to help you read and process this information. For example, I need to teach you how to look at a graph or a table of data. I need to help you understand the concepts and read between the lines. You probably cannot memorize all of the information. What you can do is to learn a framework which will suggest most of this information.

 

            The study guide [green cover] is your best review source. It contains the memorizable structures [as a list], the memorizable definitions [specifically] and the lecture outline. If you can explain each line item in the outline section, you ought to be well prepared for any exam or quiz.

 

            The workbook is designed to explain the review material, to provide a way of summarizing the information, and to provide some exposure to my type of questions. I encourage you to do the assigned exercises.

 


 Tentative Course Schedule and Reading Assignments:

Monday

Tuesday

Wednesday

Thursday

Friday

Intro, Cell Biology,

organic chem review {1,2}    [organics, pH, amino acids] 

Water, pH, & thermo-

dynamics{2}

[organics, pH, amino acids]

amino acids

{3}

[amino acid, peptides]



 

Holiday - study your amino acid structures!

protein analysis

{3}

protein 3 - D structure

{4}[amino acid, peptides]

protein function

{4}

[amino acid, peptides]



enzyme kinetics

{5}

[kinetics]

exam #1

enzyme kinetics

{5}

[kinetics]

enzyme mechanisms{6}

kinetic mechanisms

{6}

[kinetics, inhibition]

cofactors and coenzymes

{7}

[kinetics, inhibition]


carbohydrates

{8}

 [cofactors, carbohydrates]


carbohydrates

{8}

 [cofactors, carbohydrates]

exam #2

lipids

{9}

lipids and biological membranes

{9}

[lipids, signal transduction]

nucleic acids

{19}

[lipids, signal transduction]


nucleic acids

{19, ++}

ATP and bioenergetics

{10}

[bioenergetics]


glycolysis

{11}

[bioenergetics]


glycolysis

{11}

exam #3

carbohydrate metabolism

{12}

[glycolysis, other sugars]

TCA cycle

{13}

[glycolysis, other sugars]



TCA cycle

{13}

[TCA, Ox-Phos]

oxidative phosphorylation

{14}

[TCA, Ox-Phos]

Summing up/review - hurricane day

exam #4

 

FINAL EXAM

8:00 - 11:00


 

 

 

 

*The appropriate chapters in Horton et al. PRINCIPLES OF BIOCHEMISTRY (5th edition) are given in curly brackets.

 

 

[++] see page 2

 

 

 

Problem sessions for Monday and Wednesday

Date

Topic

Workbook pages

7/1

biology review; organic review; pH and pKas; Q1

            1 - 24

7/8

amino acids; peptides; Q2

⇒ 34

7/10

protein structures; oxygen binding; Q3

          ⇒ 43

7/15

enzyme kinetics - Km, Vmax, plots, inhibition; enzyme mechanisms; Q4

⇒ 57

7/17

cofactors; carbohydrates; Q5

⇒ 70

7/22

lipids; signal transduction; Q6

⇒ 77

7/24

nucleic acid structure; bioenergetics; Q7

⇒ 93

7/29

glycolysis; carbohydrate metabolism; Q8

⇒ 105

7/31

TCA cycle; Oxidative phosphorylation; Q9

⇒ 114

 

 

 

Problem sessions for Tuesday and Thursday

Date

Topic

Workbook pages

7/2

biology review; organic review; pH and pKas; Q1

1 - 24

7/9

amino acids; peptides; protein structures; oxygen binding; Q2

⇒ 43

7/11

enzyme kinetics - Km, Vmax, plots, inhibition, Q3

⇒ 53

7/16

enzyme mechanisms; cofactors; Q4

⇒ 65

7/18

carbohydrates; Q5

⇒ 70

7/23

lipids; signal transduction; Q6

⇒ 77

7/25

nucleic acid structure; bioenergetics; Q7

⇒ 93

7/30

glycolysis; carbohydrate metabolism; Q8

⇒ 105

8/1

TCA cycle; oxidative phosphorylation; Q9

⇒ 112