- BIOLOGY
3521-- BIOCHEMISTRY
- Fordham University -- Spring
1999
LECTURE SUPPLEMENTS EXAM
I
- Notes, Readings, WWW Tutorials, and
other Links
Updated
- 2/9/99
Lectures
|
Exam I
|
Exam II
|
Exam III
|
Exam
IV
|
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Lecture 1
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Lecture 10
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Lecture 18
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Lecture 25
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Lecture
2
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Lecture 11
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Lecture 19
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Lecture 26
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Lecture
3
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Lecture 12
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Lecture 20
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Lecture 27
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Lecture
4
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Lecture 13
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Lecture 21
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Lecture 28
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Lecture
5
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Lecture 14
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Lecture 22
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Lecture 29
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Lecture 6
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Lecture 15
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Lecture 23
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Lecture 30
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Lecture 7
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Lecture 16
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Lecture 24
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Lecture 31
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Lecture
8
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Lecture 17
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Review/Exam
|
Lecture 32
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Lecture
9
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Review/Exam
|
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Lecture 33
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Review/Exam
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|
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Lecture 34
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Lecture 35
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Lecture 36
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Review/Exam
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Lecture
1 -- Intro. to Biochemistry & Types & Organization of
Cells
Class Material at the Web
Site
On Reserve in the Library
- Chapter 1 of Horton et al. (1996) "Principles of
Biochemistry" -- Provides general overiew of biochemistry with
a discusion of biopolymers, cells, and cell structures
- Chapter 1 of Voet and Voet (1995) "Biochemistry" --
More in depth discussion of same topics plus phylogeny,
metabolism, origin of life, and biochemical literature
Videos at the Electronics Media
Center
- Working with Proteins
- Model Organisms
- Mouse, Nematode, Arabidopsis, Drosophila, Lambda, and
Yeast
Internet Recommendations
- As of the end of January '99, the author removed this
material from the Web
- Course/Tutorial on Cell Biology created and
maintained by Mark Dalton, Computational Biology Center,
University of Minnesota Medical School. This a great site to
review your cell biology with respect to cells!
- Chapter 1: Types of Cells
- Chapter 2: Organization and Components of Cells
-
Lecture
2 -- Chemical bonds, associations, and functional
Groups
Class Material at the Web
Site
On Reserve in the Library
- Chapter 1 of Horton et al. (1996) "Principles of
Biochemistry" -- Provides general overiew of biochemistry with
a discusion of biopolymers, cells, and cell structures
- Chapter 1 of Voet and Voet (1995) "Biochemistry" --
More in depth discussion of same topics plus phylogeny,
metabolism, origin of life, and biochemical literature
Internet Recommendations
Homework Suggestions on the
Internet
- Homework Problems and answers for a chemistry review from
MIT
-
Lecture
3 -- Water and pH
Class Material at the Web
Site
On Reserve in the Library
- Chapter from "Problem Solving in Biochemistry" --
"Acid-base Chemistry" , In depth presentation of lecture
topics with derivation of equations and many problems and
solutions illustrating the concepts and calculations
- Chapter 21 from "Basic Concepts in Biochemistry: A
Student's Survival Guide" -- pH, pKa, pProblems
- Good intuitive explanations if you are having trouble with
the material and need some math support
- Chapter 2 of Voet and Voet (1995) "Biochemistry" --
Another treatment of aqueous solutions
Internet Recommendations
- Chemistry
Review for biologists at MIT -- Very good and
Useful
- The
Acid and Base\pH Tutorial at the University of British
Columbia
- Use only if you see that it will help you with minimal
use and you are very chemically oriented and good with
Netscape
COURSE HOMEWORK (STRONGLY
RECOMMENDED)
- These links are built into the lecture notes and are placed
here again for your use
- Some simple pH calculation problems (with answers) from
FIU illustrating the
- Homework Problems
and answers
on pH, water, and amino acids from FIU
- Use of Henderson Hasselbalch equation from Florida
International University (FIU)
- Study set #1 -- pH,
pKa, and Henderson-Hasselbalch
-
Lecture 4
-- Amino acids, peptide bond, and levels of protein
structure
Class Material at the Web
Site
On Reserve in the Library
- Study Aid: See Chapter 3 "Amino Acids and the Primary
Structures of Proteins" from Horton et al (1996) "Principles of
Biochemistry" (Prentice Hall) for more information or
clarification (Text on Reserve in Walsh Library - Science Desk)
Internet Recommendations
COURSE HOMEWORK (STRONGLY
RECOMMENDED)
COURSE HOMEWORK involving structures and
graphics
-
- Lecture
5 -- Protein structure and folding
Class Material at the Web
Site
On Reserve in the Library
- Study Aid: See Chapter 4 "Proteins: Three-Dimensional
Structure and Function" (particularly the summary) from Horton et
al (1996) "Principles of Biochemistry" (Prentice Hall) for more
information or clarification (Text on Reserve in Walsh Library -
Science Desk)
Internet Recommendations
- See links to structures in lecture notes (particularly
for Chemscape Chime and Kinemage Structures)
- For Another treatment of simple aspects of primary through
quarternary structure of proteins with static images see the
MIT
Hypertext Chapter of Protein Structure
COURSE HOMEWORK involving structures and
graphics
REQUIRED
-
- Lecture
6 -- Protein structure cont. and structure
prediction
Class Material at the Web
Site
On Reserve in the Library
- Chapter 2 from "Basic Concepts in Biochemistry: A Student's
Survival Guide" -- Protein Structure
- Brief and good intuitive explanations for protein structure
discussed in class (only 21 short pages) with aids for studying
material
- Study Aid: See Chapter 4 "Proteins: Three-Dimensional
Structure and Function" (particularly the summary) from Horton et
al (1996) "Principles of Biochemistry" (Prentice Hall) for more
information or clarification (Text on Reserve in Walsh Library -
Science Desk)
Internet Recommendations
- See links to structures in lecture notes (particularly
for Chemscape Chime and Kinemage Structures)
- For Another treatment of simple aspects of primary through
quarternary structure of proteins with static images see the
MIT
Hypertext Chapter of Protein Structure
Videos at the Electronics Media
Center
- Working with Proteins
- Solving Crystal Structures
COURSE HOMEWORK involving structures and
graphics
COURSE HOMEWORK (STRONGLY
RECOMMENDED)
-
- Lecture
7 -- Analysis of proteins
Class Material at the Web
Site
Internet Recommendations
- See links in lecture notes
Videos at the Electronics Media
Center
- Working with Proteins
- Fractionating a Cell
- Column Chromatography
- Determining Mass and Shape
- Activity Assays (Best to watch for enzyme section of course
= Exam II)
On Reserve in the Library
- Study Aid: Section 3·6 Protein Purification
Techniques from Chapter 3 of Horton et al (1996). "Principles of
Biochemistry" (Prentice Hall) for more information or
clarification (Text on Reserve in Walsh Library - Science
Desk)
COURSE HOMEWORK (STRONGLY
RECOMMENDED)
-
- Lecture
8 -- Analysis of proteins
Class Material at the Web
Site
On Reserve in the Library
- Study Aid: Sections from Chapters 3 and 4 in Horton et
al "Principles of Biochemistry" for more information or
clarification (Text on Reserve in Walsh Library - Science Desk)
- 3·7 Amino Acid Composition of Proteins
- 3·8 The Sequence of Amino Acid Residues
- 3·9 Protein Sequencing Strategies
- Chapter 3 Summary
- 4·2 Methods of Determining Protein Structure
- Chapter 4 Summary
Internet Recommendations
- See links in lecture notes
Videos at the Electronics Media
Center
- Working with Proteins
- Sequencing a Protein
- Solving crystal structures (Not Covered in Class)
COURSE HOMEWORK (STRONGLY
RECOMMENDED)
-
Lecture 9
-- Protein conformational changes and Allosterics:
Hemoglobin
Class Material at the Web
Site
On Reserve in the Library
- Study Aid: Sections from Chapter 4 (Proteins:
Three-Dimensional Structure and Function) in Horton et al
"Principles of Biochemistry" for more information or clarification
(Text on Reserve in Walsh Library - Science Desk)
- 4·12 Myoglobin, a Globular Protein
- 4·13 Hemoglobin, a Globular Protein Possessing
Quaternary Structure
- 4 ·14 Globular Protein Function: Oxygen Binding to
Myoglobin and Hemoglobin
- Chapter 4 Summary
COURSE HOMEWORK (STRONGLY
RECOMMENDED)
Supplementary: Hemoglobin and a Review
Tutorial on Protein Structure using Hemoglobin
-
EXAM
I
Lectures 1-9 - Study questions,
homework, review guides and sample exams
See the questions or suggestions provided for each
lecture
Many of the most important and valuable ones are provided
here again:
- Chapter from "Problem Solving in Biochemistry" --
"Acid-base Chemistry"
- On Reserve in Walsh Science Library:
- Many problems and solutions illustrating the concepts and
calculations
- STRONGLY RECOMMENDED
-
- pH, water, and amino acids
- Some simple pH calculation problems (with answers)
illustrating the
- Homework Problems
and answers
on pH, water, and amino acids from FIU
- Use of Henderson Hasselbalch equation from Florida
International University (FIU)
- Homework problems
and answers
on pKa and amino acids (FIU)
-
- Amino acids, peptides, protein structure, and conformation
changes
- MOLECULAR GRAPHICS
REVIEW
- Molecular Graphics
- Homework Problems
- Study
Questions & Answers
Relating to Analysis of Peptides and their sequence
determination
- Handout: Problems and
Answers for Amino Acids, Peptides, and Analysis of
Proteins
-
Last Year's Fordham Exam I
- Fordham BIRU 3521 Spring '98 Exam I (To see these in
your browser you need Adobe Acrobat and the PDF Viewer
Plug-in)
-
- Sample Exams from other courses with similar topic
converage:
- Other Biochemistry Course Exams
- If you do best by working problems/answers and taking
practice exams in preparing for an Exam, Exams from other
similar Biochemistry Courses are provided below
- NOTE: Ignore questions corresponding to material we did
not discuss or cover or that I have not emphasized
- Exams from Biochem 460 at Arizona
- Exams from Biochem 3033 at FIU
- Exam I online
test
- Cells, water, pKa, water, amino acids, and proteins,
and protein analysis
- Exam II online
test
- Bioenergetics, oxygen carriers, other protein info,
enzymes, and enzyme kinetics
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