72120 biochemistry of the cell
TRANSCRIPT
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72120 Biochemistry of the cell
Introduction
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Basic facts 1 • Teachers:
– Isaiah (Shy) Arkin: [email protected] – And a bunch of helpers.
• Teaching assistants: – Raphael Alhadeff: [email protected] – Liat Avrahami: [email protected]
• Lectures: – Sunday 14:00-15:45. – Monday 10:00-11:45.
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Basic facts 2
• Tutorials (starting next week): – Group A Wednesday, 8:00-9:45. – Group B Thursday, 8:00-9:45. – Group C Wednesday 18:00-19:45. – Group D Thursday 14:00-15:45.
• Recommended Textbook: – Biochemistry 6th edition, Berg, Tymoczko & Stryer
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Basic facts 3 • The course’s homepage is: http://teachline.ls.huji.ac.il/72120/. In
it one will find the lecture notes. • The tutorials will cover what was covered in the lectures and
materials for self-study. • There will be 4 mini exams that will constitute 8% of the final
grade. • The exam covers material that was covered in the lectures, in
the tutorials and those given for self-study. • The exam will represent 92% of the grade of the course.
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The “mini-exams” will take place as follows: Location: Rashal Time: 11:30-11:45 on Mondays Dates: 1/11/10, 22/11/10, 13/12/10 and 10/1/11.
The grading will be as follows: 0-50: 0 points 50-75: 1 point 75-100: 2 points.
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Cell Biology Introduction
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Amino acids
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Proteins in short
• The most versatile macromolecule. • Linear polymers of amino acids. • Many different functional groups. • Can form large complexes • Can be rigid or flexible.
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Amino acids 1
• There are 20 common, genetically encoded amino acids.
• 2 very uncommon, genetically encoded amino acids.
• Large number of “non-standard” amino acids that are not genetically encoded.
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Amino acids 2
• α-amino acids. • L isomer (nearly always S). • There are ca. 20 of them. • Used in all organisms. • They can be modified.
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N
H
O
Se
H
Genetically encoded rare amino acids 1: Selenocysteine
• The amino acid is not found except in proteins, where it is involved in redox reactions (for example, glutathione peroxidase, tetraikiodothyronine 5' deiodinase and formate dehydrogenase).
• The specific tRNA is 1st amino-acylated to Ser and then the Ser is modified to Selenocysteine.
• Why some codons are used and others not seems to depends on additional cis elements.
• Since Selenocysteine is so active the thought is that it was once very popular but as the atmosphere became oxidizing it became a disadvantage.
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N
H
N
H
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O
N
H
O
Genetically encoded rare amino acids 2: Pyrrolysine
• Found so far only in methylamine methyltransferase genes of Methanosarcina barkeri
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Peptide bond cleavage ���by hydrolysis
• The peptide bond is much more stable than an ester bond however: • Thermodynamics: the equilibrium constant for hydrolysis of a peptide bond (the reverse of the condensation reaction shown above) favors hydrolysis by a factor of 103 to 104. Thus, the peptide bond is unstable with respect to its hydrolysis products. • Kinetics: the rate of peptide bond hydrolysis under physiological conditions is very slow; the half-time for the reaction can be years. Thus, the peptide bond is stable when considered on a physiological time scale. • In acidic and basic conditions the peptide bond is hydrolyzed. It is for this reason that our stomachs are acidic to facilitate protein degradation. • Insects utilize a basic stomach.
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C-N 1.49Å C=N 1.27Å
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