General Info
Course
BIOCHEMISTRY I / BIOL154
Year of study
1
Semester
Spring, B (First year undergraduates)
Type of Course
Core
Number of Credits
4 (ECTS: 6)
Department
Biology, University of Crete
Section
Biochemistry, Molecular Biology, Cellular and Developmental Biology
Instructor
Charalampos (Babis) Spilianakis, PhD
Office
IMBB-FORTH, A204
spiliana@imbb.forth.gr, spiliana@biology.uoc.gr
Phone
2810-391163 (office), 2810-391173 (lab)
Office hours
09.00 am - 21.00 pm
Lectures
Biology Auditorium I, Monday 16.00-18.00, Friday 16.00-18.00
During lectures we will discuss principles, outline goals, and present demonstrations. Your attendance at all lectures is vital to your success in this course. You should read the textbook assignment prior to lecture and take clear notes during lecture. I fully encourage and expect student participation during lectures.
Teaching Methods
Lectures (PowerPoint Presentations), Videos & narrated animations, Student Response System (iRespond), Multiple Choice Questions & Solved Problems
Language of Instruction
Greek
Assessment methods
Written Examination, written Midterm exam, Student Response System (iRespond)
Midterm exams
There will be a midterm exam which is not obligatory and can only be additive to the final exams' grade.
Grading
An exam is considered successful if you get at least 50/100 points.
Regrading
Any request for a regrade must be made within one week of receiving your graded exam. Contact the instructor preferably by email to arrange for an appointment and go through your script. You will also get a printout with the answers of the exams' subjects.
Attendance
Attendance at all lecture sessions is expected. If a session is missed, it is the student’s sole responsibility to make up any work missed.
Academic Honor Principle
Students are expected to observe the University’s Code of Student Conduct. Cheating on examinations and/or problem sets is not acceptable and will be met with zero tolerance!
Prerequisites
There are no prerequisites for this course.
Instruction Materials
Textbook choice I
BIOCHEMISTRY - W.H. Freeman, 7th edition,
BERG M.J., TYMOCZKO L.J., STRYER L., 7th edition
Greek version: Crete University Press, c2014 (ISBN-13: 978-960-524-432-3, Εudoxus Code: 41954660)
Conceptual Insights, Living Figures, Animated Techniques, Online Quizzing, Flashcards, Glossary, Biochemistry on the Web, General Chemistry Review.
Textbook choice II
Lehninger Principles of Biochemistry - macmillan education, 5th edition, c2009
David L. Nelson, Michael M. Cox
Greek version: Paschalidis Medical Publications (Εudoxus Code: 13257016)
Animated Enzyme Mechanisms, Animated Biochemical Techniques, Molecular Structure tutorials, Living Graphs, Interactive Quizzes, Weblinks, Molecular Structures, Lecture Companion Art.
Textbook choice III
Textbook of BIOCHEMISTRY with clinical correlations 7e
T.M.Devlin, John Wiley & Sons Inc., c2011
Greek version: Paschalidis Medical Publications (Εudoxus Code: 13256908 & 13256618)
Animated Figures, Guided Explorations, Interactive Exercises.
Lectures Download
Each academic year the Powerpoint presentations in either .pptx format (Microsoft Office 2011) or .pdf format will be uploaded upon the completion of each lecture (material included in an individual lecture's file may be covered in more than a 2 hours session).
Downloads from previous Academic Years
Final Exams
Description
Introduction to BIOL_154 Biochemistry I course. All you would like to know about the lecturer and the course.....
Download: Powerpoint presentation (pdf).
Description
Introduction to cells
Microscopy
Cell architecture
Life's common mechanisms
Download: Powerpoint presentation (pdf).
Description
The molecular design of life
Biochemical unity underlies Biological diversity
DNA illustrates the interplay between form and function
Chemical components of cells
What are macromolecules
Chemical bonds and groups
An outline of some of the types of sugar
Fatty acids and other lipids
The 20 amino acids found in proteins
A survey of the nucleotides
The principal types of weak noncovalent bonds
Download: Powerpoint presentation (pdf).
Description
Water
Weak interactions in aqueous systems
Hydrogen bonding gives water its unusual properties
Water forms hydrogen bonds with polar solutes
Water interacts electrostatically with charged solutes
Entropy increases as crystalline substances dissolve
Nonpolar gases are poorly soluble in water
Nonpolar compounds force energetically unfavorable changes in the structure of water
van der Waals interactions are weak interatomic attractions
Weak interactions are crucial to macromolecular structure and function
Solutes affect the colligative properties of aqueous solutions
Ionization of Water, weak Acids and Weak Bases
Pure water is slightly ionized
The ionization of water is expressed by an Equilibrium Constant
The pH scale designates the H+ and OH- concentrations
Weak acids and bases have characteristic acid dissociation Constants
Titration curves reveal the pKa of weak acids
Buffering against pH changes in Biological Systems
Buffers are mixtures of weak acids and their conjugate bases
The Henderson-Hasselbalch equation relates pH, pKa and Buffer concentration
Weak acids or bases buffer cells and tissues against pH changes
Water as a Reactant
The fitness of the Aqueous environment for living organisms
Download: Powerpoint presentation (pdf).
Description
Protein Composition and Structure
Proteins are built from a Repertoire of 20 Amino Acids
Primary Structure: Amino Acids are linked by Peptide bonds to form Polypeptide Chains
Secondary Structure: Polypeptide Chains can fold into regular structures such as the Alpha Helix,
the Beta Sheet and Turns and Loops
Tertiary Structure: Water-soluble proteins fold into compact structures with Nonpolar cores
Quaternary Structure: Polypeptide chains can assemble into Multisubunit Structures
The Amino Acid sequence of a Protein determines its Three-Dimensional Structure
Download: Powerpoint presentation (pdf).
Description
Exploring Proteins and Proteomes
The purification of Proteins is an essential first step in understanding their Function
Amino Acid sequences can be determined by automated Edman degradation
Immunology provides important techniques with which to investigate proteins
Mass Spectrometry provides powerful tools for protein characterization and identification
Three-dimensional protein structure can be determined by X-ray crystallography and NMR spectroscopy
Download: Powerpoint presentation (pdf).
Description
Enzymes: Basic Concepts and kinetics
Enzymes are powerful and highly specific Catalysts
Free Energy is a useful thermodynamic function for understanding Enzymes
Enzymes accelerate reactions by facilitating the formation of the Transition State
The Michaelis-Menten equation describes the kinetic properties of many enzymes
Enzymes can be inhibited by specific molecules
Download: Powerpoint presentation (pdf).
Description
Catalytic Strategies
Proteases facilitate a fundamental difficult reaction
Chymotrypsin
Restriction enzymes perform highly specific DNA-cleavage reactions
Nucleoside Monophosphate kinases catalyze phosphoryl-group transfer without promoting hydrolysis
Download: Powerpoint presentation (pdf).
Description
DNA, RNA and the Flow of Genetic Information
A Nucleic Acid consists of four kinds of Bases linked to a Sugar-Phosphate Backbone
A Pair of Nucleic Acid Chains with Complementary Sequences can form a Double-Helical Structure
DNA is Replicated by Polymerases that take instructions from Templates
Gene Expression is the Transformation of DNA Information into Functional Molecules
Amino Acids are encoded by groups of Three bases starting from a Fixed Point
Most Eukaryotic Genes are Mosaics of Introns and Exons
Download: Powerpoint presentation (pdf).
Description
Exploring Genes and Genomes
The exploration of Genes relies on key tools
Recombinant DNA technology has revolutionarized all aspects of Biology
Complete genomes have been sequenced and analyzed
Eukaryotic genes can be manipulated with considerable precision
Download: Powerpoint presentation (pdf).
Description
Carbohydrates
Monosaccharides are aldehydes or Ketones with multiple hydroxyl groups
Complex carbohydrates are formed by the linkage of monosaccharides
Carbohydrates can be attached to proteins to form glycoproteins
Lectins are specific carbohydrate-binding proteins
Download: Powerpoint presentation (pdf).
Description
Metabolism: Basic Concepts and Design
Metabolism is composed of many coupled, interconnecting reactions
ATP is the universal currency of free energee in biological systems
The oxidation of carbon fuel is an important source of cellular energy
Metabolic pathways contain many recurring motifs
Download: Powerpoint presentation (pdf).
Description
Glycolysis
Glycolysis
Feeder pathways for Glycolysis
Fates pf Pyruvate under anaerobic conditions: Fermentation
Download: Powerpoint presentation (pdf).
Description
Gluconeogenesis
Pentose phosphate pathway of Glucose oxidation
Download: Powerpoint presentation (pdf).
Description
The Citric Acid cycle
Production of acetyl-CoA
Reactions of the Citric Acid cycle
Regulation of the Citric Acid cycle
Download: Powerpoint presentation (pdf).
Description
Download: Powerpoint presentation (pdf).
