Download - Biochemistry Lectures
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proteins
nucleic acids
metabolism
CHEMISTRY 251/Fall 2012Instructor: Prof. Barry S. Cooperman 358 Chemistry [email protected]: MWF 9 am in room Chem 102Prerequisite: Chem 102; Chem 241 (can be taken concurrently)Required Textbook: Fundamentals of Biochemistry. 4th edition (2012) - Voet, Voet, and Pratt Office hours: arranged by email
Lecture schedule (approximate) Sept 5 – Introduction - Chapters 1, 2Sept 7 - 12 Amino acids and protein primary structure Chapters 4, 5Sept 14 – 21 Protein structure and function Chapters 5, 6Sept 24 – 26 Enzymes, Chapters 11 and 12Sept 28, Oct 1 – Other Protein Functions chapters 7, 28Oct 3 Exam 1Oct 5-12 Nucleotides, Nucleic Acids and Nucleic Acid Structure - Chapters 3, 24Oct 15 - 19 DNA Replication - Chapter 25Oct 22 – 26 DNA Transcription Chapter 26 Oct 29 – Nov. 2 Translation Chapter 27Nov 5 Regulation of Gene Expression, small RNAs Chapter 28 Nov 7 Exam 2 Nov 9 Metabolism (general) Chapter 14Nov 12 – 16 Carbohydrates, Glucose and Glycogen Metabolism - Chapters 8, 15 & 16Nov 19, 21 Lipids, membranes, and lipid metabolism Chapters 9, 10, 20Nov 26 – Nov 30 - Citric Acid Cycle, Electron Transport, Oxidative Phosphorylation - Chapters 17 & 18Dec 3 - Exam 3Dec 5, 7 - Amino Acid Metabolism, Mammalian Metabolism – Chapters 13, 21, 22
-weekly recitation –voluntary – times and locations to be announced-There will be three hourly exams and one final. -Grades will be based on 100 points for each hourly exam and 150 points for the final. -Lecture notes and power point files will be posted on Blackboard page for Chem 251-Make-up lectures: I will be unable to lecture on Wed Sept 12 and Wed Sept 26. To make-up for the time lost, the following lectures will begin at 8:30 am instead of 9:00 am: Mon Sept 10, Fri Sept 14, Mon Sept 24, Fri Sept 28.
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How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?
Erwin Schrödinger, What is Life?
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MetabolismSum of chemical and physical reactions carried out by cell
Catabolism - breakdown of nutrients and cell components to generate energy and common precursors (building blocks); reactions are generally exergonic oxidations:- GAnabolism - synthesis of biomolecules - endergonic :+ G
Obligate aerobes - use O2 for oxdtn; animalsObligate anaerobes - O2 toxic; use other oxidantse.g., sulfate, nitrate -some bacteriaFacultative anaerobes - can use O2 or other oxidants - e.g., E. coli
Energy storage -High energy phosphate bonds; ATP: thioestersReduced cofactors: NADH, NADPH, FADH2
Generated by catabolic processes;Consumed by anabolic processesIntercoverted by oxidative phosphorylation
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The Central Dogma
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General structural formula for -amino acids
Zwitterionic form
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Pag
e 66
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Cystine
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Greek letter convention for naming side chains
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Titration curve of glycine
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Condensation of two -amino acids to form a dipeptide
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The tetrapeptide Ala-Tyr-Asp-Gly
Note that within a peptide, the -amino and -carboxyl ionizationsare suppressed, except for the amino terminus and the carboxyl terminus. However, side-chain ionizations are maintained.
Aminoterminus
Carboxyl terminus
Side chain ionization
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Ionizable side chains
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Isoelectric Point of a Protein - no net charge -net charge (pH 7) = Arg + Lys + fHHis) - Asp + Glu + fCCys)-example shown is basic protein; (Arg + Lys) > (Glu + Asp + Cys)-so reaching isoelectric point requires deprotonation of some Lys residues (pKa 10.5)-for acidic protein: (Arg + Lys + His) < (Glu + Asp) - so reaching isoelectric point requires His protonation (pKa 6), and possibly some Glu or Asp protonation (pKa 4.5)
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Convention for naming the enantiomers of amino acids
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A tetrahedral C with four different substituentsis chiral; has a nonsuperposable mirror image
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Modified amino acid residues occurring in proteins
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Biologically Active Compounds derived from Amino Acids
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Insulin
Intra- and inter-chain disulfides (cystines)
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Sizing ProteinsMALDI-TOF MASSSPECTROSCOPYMANN ET AL.
Annu. Rev. Biochem. 2001. 70:437–73
Figure 1 Schematic of MALDI process and instrument. (A) A sample cocrystallized withthe matrix is irradiated by a laser beam, leading to sublimation and ionization of peptides. (B) About 100–500 ns after the laser pulse, a strong acceleration field is switched on (delayed extraction), which imparts a fixed kinetic energy to the ions produced by the MALDI process. These ions travel down a flight tube and are turned around in an ion mirror, or reflector, to correct for initial energy differences. The mass-to-charge ratio is related to the time it takes an ion to reach the detector; the lighter ions arrive first. The ions are detected by a channeltron electron multiplier.
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MALDI-TOFMS of ribonucleotide reductase large subunit.Secondary peaks correspond
to a doubly charged mass.P. Foo, 2002
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Myoglobin: Shown are mass/chargeratios
Positive charges due to Arg and Lys residues
Sizing proteins by Electrospray Ionization (ESI) Mass spectrometry
Fragmentation of Protein Into Peptide Fragments: Tandem Mass Spectrometry
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Gel electrophores
is
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Sucrose density gradient
ultra
€
s =v
ω 2r=
M(1− v_
ρ )D
RT
D M-1/3; s M2/3
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Shape dependence}
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RS-SR' + R"SH RSH +R'S-SR"
R'S-SR" + R"SH R'SH +R"S-SR"
RS-SR' = polypeptide; R"SH = 2-mercaptoethanol1
2RSH + ICH2CO2
- RSCH2CO2- + I- + H+
1
2
If no disulfides, start here
Protein Sequencing-1
Disulfide reduction
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Protein Sequencing-2
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Chemical cleavage - CNBr
At Mets
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Process can be repeated on new N-terminus; can be repeated up to ~50 cycles
N-terminal Sequencing:The Edman Degradation
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typical outputfrom amino acidanalysis
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Sequencing with overlapping fragments
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Tandem Mass Spectrometry for Sequencing
1) Proteinase digestion of protein
2) ESI-MS to generate peptide ions from digest (MS-1)
3) Collision cell to generate fragments of each ion
4) MS analysis of fragment ions (MS-2)
5) In this example, Peptide P3 fragments into F1 - F5 which are overlapping, allowing sequence to be deduced.