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國立交通大學生物科技學系蘭宜錚老師 1
Lecture 1Introduction & Scope of Biochemistry
Chapter 1, Biochemistry 4th edition, Mathews, Van Holde, Appling, Anthony‐Cahill. Pearson ISBN:978‐0‐13‐800464‐4
DBT2117: Biochemistry (I) (English course)
Week Topics
1 Chapter 1 The Scope of Biochemistry
2 Chapter 1 The Scope of Biochemistry
3 Chapter 2 The Matrix of Life, Chapter 3 The Energetics of Life
4 Chapter 4 Nucleic Acids
5 Chapter 4 Nucleic Acids
6 Exam 1
Course Syllabus
國立交通大學生物科技學系蘭宜錚老師 2
Week Topics
7 Chapter 5 Introduction to Proteins
8Chapter 5 Introduction to Proteins & Chapter 6 The Three‐Dimensional Structure of Proteins
9 Chapter 6 The Three‐Dimensional Structure of Proteins
10 Chapter 7 Protein Function and Evolution
11 Chapter 8 Contractile Proteins and Molecular Motors
12 Exam 2
Course Syllabus
Week Topics
13 Chapter 9 Carbohydrates: Sugars, Saccharides, Glycans
14 Chapter 10 Lipids, Membranes, and Cellular Transport
15 Chapter 10 Lipids, Membranes, and Cellular Transport
16 Chapter 11 Enzymes: Biological Catalysts
17 Chapter 12 Chemical Logic of Metabolism
18 Exam 3
Course Syllabus
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Grading policy
• Final grade will be the average of three exams
• We will review the exam in details.• Any mistakes in grading must be submitted for regrade during the review session• No regrades will be considered after the review session
• Curves in the final grade will follow the university’s rule on undergraduate course having anpassing average score of 78 ± 3.
Introduction – What is biochemistry?
• Biochemistry is the branch of science that seeks to describe the structure, organization, andfunctions of living matter in molecular terms.
• The GOAL of biochemistry is to understand life at the molecular level.• The Chemistry of life
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Biochemistry can be divided into three principal areas:
1. The structural chemistry of the components of living matter and relationships ofbiological function to chemical structure.
2. Metabolism, the totality of chemical reactions that occur in living matter.(Biochemistry II)
3. Genetic biochemistry, the chemistry of processes and substances that store and transmitbiological information. (Molecular genetics)
•This third area is also the province of molecular genetics, a field that seeks to understandheredity and the expression of genetic information in molecular terms.
Introduction – What is biochemistry?
4 major biomolecules
• This course will discuss in details the properties and functions of the major biomolecules
• 4 major classes of biomolecules:
• Carbohydrates (energy storage, structure supports)
• Proteins (Enzymes, structural supports)
• Lipids (Fats, cellular membranes)
• Nucleic acids (DNA, RNA)
國立交通大學生物科技學系蘭宜錚老師 5
Carbohydrates (energy storage, structure supports)
Carbohydrates
Proteins
Proteins (Enzymes, structural supports, many more diverse functions)
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Lipids
Lipids (Fats, cellular membranes, hormones)
Nucleic acids
Nucleic acids (DNA, RNA)
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Elements in life
Carbon, Hydrogen, Oxygen, Nitrogen are the major ingredients of life (DNA/RNA, proteins, sugars, fats..)
Phosphorus is in found DNA (as well as many cellular metabolites‐chemicals in life)
Sulfur is found in proteins.
Bonding ability of carbon: why carbon is the most significant element
Carbon, Oxygen, Hydrogen, & Nitrogen together make up more than 99% of most cells.
Hydrogen: can only form 1 bondOxygen: 1, or 2 bondsNitrogen: 1, 2, or 3 bondsCarbon: 1, 2, 3, or 4 bonds.
Some common bonds found in biology are shown in the right.
Covalent bonds
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Common functional groups in biochemistry
Carbon functional groups Oxygen functional groups
(these are less frequent)
Functional groups are groups of atoms added to carbon skeleton that have specific properties.
Common functional groups in biochemistry
Nitrogen functional groups
Sulfur functional groups
Phosphur functional groups
國立交通大學生物科技學系蘭宜錚老師 9
Common functional groups in biochemistry
Most biomolecules have multiple functional groups within them.
For example, Acetyl‐CoA (a common metabolite used to both synthesize lipids and respiration)
*note: Metabolites = chemical compounds found in the cell
Chirality
Biochemistry is extremely structure‐oriented
Molecules with the same empirical formula may have different chirality – Enantiomers, Diastereomers, etc. are DIFFERENT compounds
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Biological macromolecules and their monomers
Macromolecule Monomer Linkage
• Protein amino acid peptide(amide)
• Polysaccharide monosaccharide glycoside(ether)
• Nucleic acids nucleotide phosphodiester
• Lipids (triglycerides) fatty acids ester
Many biomolecules are macromolecules (polymers of high molecular weight)
Below is a chart of the common macromolecules found in life:
Common functional groups in biochemistry
Cellulose is a major component of plant biomass. It is a polymer of glucose (a sugar)
Looking at glucose in its linear form… what functional groups does it have?
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Common functional groups in biochemistry
Besides the Adenine group, what other groups are present in dAMP (a monomer of DNA)?
How about dATP (the real building block of DNA)?
Common functional groups in biochemistry
A peptide bond is an amide bond between 2 amino acids
In addition to the phenol functionality, what other functional groups are present?
phenol
國立交通大學生物科技學系蘭宜錚老師 12
Bonding and resonance structures
Resonance structure = a way to describe the delocalization of electrons within a molecule.
The electrons (red) are evenly distributed among the two Oxygen atoms. This helps to provide stability for the molecule
The more “positions” that electrons can move to, the more resonance stabilization the molecule has.
Reactivity & Stability
Generally speaking, the more stable a chemical/compound, the less reactive it is.
If a compound undergoes a reaction can generate a more stable product, then that compoundis more reactive than its product
ATP is a cellular “energy carrier” used to drive chemical reactions
H2O
Lots of negative charges = repulsion ΔG'° is ‐30.5 kJ/mol
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Free energy and direction of chemical equilibrium
• The Gibbs Free Energy is:
where ([C]c[D]d)/([A]a[B]b) we call Q the reaction quotientProducts / substrates
• At equilibrium, Q = Keq, and ΔG = 0,therefore‐ ΔGo = RT ln Keq
aA + bB cC + dD
For a reaction of:
Acid dissociation constant
Same idea applies also to acid dissociation (proton moving from one molecule to H2O)
Any acid dissociation can be viewed as this:
When working under dilute conditions (Water concentration doesn’t change)
Since this number could be quite large (or small) depending on the compound, its easier to use:
The lower the pKa, the more likely that proton (H+) is removed from this compound
Here H+ = H3O+
How easy is the H+ removed from the compound (HA)? ‐ That depends on how STABLE its conjugate base (A‐) is
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pKa does not only apply to “acids”
Every hydrogen (proton) on a compound has a pKa
Understanding this concept is very important for understanding enzymes and enzyme mechanism
Increasin
g stability after d
eprotonatio
nDecreasin
g stability
Chemical evolution: Miller–Urey experiment
"Miller‐Urey experiment‐en" by GYassineMrabetTalk✉This vector image was created with Inkscape.iThesource code of this SVG is valid. ‐ Own work from Image:MUexperiment.png.. Licensed under CC BY‐SA 3.0 via Commons ‐ https://commons.wikimedia.org/wiki/File:Miller‐Urey_experiment‐en.svg#/media/File:Miller‐Urey_experiment‐en.svg
To simulate abiotic (nonbiological) origin of biomolecules, Stanley Miller & Harold Urey in 1953 observed the production of organic compounds, some amino acids, hydroxyacids, etc, from their reaction set up shown to the left
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Central Dogma
Current understanding of central dogma
https://commons.wikimedia.org/wiki/File:Extended_Central_Dogma_with_Enzymes.jpg
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Which came first? Protein or DNA?
The current understanding is that most likely RNA came first. RNA is both capable of maintaining information AND catalysis
(even capable of forming peptide bonds)
Through evolution, eventually catalysis function went to proteins (because proteins are more versatile), and information conservation went to DNA (because DNA is more stable)
Possible “RNA world” scenario
Deoxyribonucleotide ribonucleotide(for making DNA) (for making RNA)
Sizes of cellular biomacromolecules
The DNA from one chromosome has a mass of ~20 billion Daltons
Proteinmolecules have masses of 10,000 to 1 million Daltons
1 Dalton (Da) = 1 amu = 1 g/mol
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1. Program ‐ organized plan for constitution and regeneration of an organism (e.g., DNA).
2. Improvisation ‐ the ability of living matter to change the program to assure survival as thesurroundings change.
3. Compartmentalization ‐ the ability of an organism to separate itself from the environment,such as with membranes.
Koshland’s seven “pillars of life”
4. Energy ‐ living matter must create complexity in order to sustain the program and the otherpillars of life.
5. Regeneration ‐ the ability to compensate for the inevitable wear involved in maintaining aphysical state far from equilibrium.
6. Adaptability ‐ the capacity of an organism to respond to environmental changes.
Koshland’s seven “pillars of life”
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7. Seclusion ‐ the metabolic processes and pathways must operate in isolation from oneanother, even though they may take place within the same compartment of a cell.
Koshland’s seven “pillars of life”
Interconnected with all seven pillars of life is the function of:
Semipermeable membranes ‐ surround cells and intracellular organelles, such as the mitochondria, maintaining
Homeostasis ‐ a condition in which the chemical composition of a biological system is held constant.
Evolution
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Evolution
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