16-370_Final_exam_review

16-370_Final_exam_review - BIO/CHM 370/670 Review Sheet for...

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BIO/CHM 370/670 Review Sheet for Final Exam Chapter 1: Foundations of biochemistry Important concepts: - Biochemistry builds on many disciplines! Know : - Functional groups o o Great variety of functional groups - Differences between prokaryotes & eukaryotes o Prokaryote Organisms without a cell nucleus or any other membrane-bound organelles. Most are unicellular, but some prokaryotes are multicellular. o Eukaryote Organisms whose cells are organized into complex structures by internal membranes and a cytoskeleton. The most characteristic membrane bound structure is the nucleus. Animals , plants, fungi, and protists. Chapter 2: Water Important concepts: - Weak (noncovalent) forces are important for the properties of biomolecules in an aqueous environment. o Active role in stability and catalytic properties of biomolecules - Acids and bases can be quantitatively analyzed. - Buffers (mixture of weak acid and salt of its conjugate base) resist pH change. - Water can participate in chemical reactions. Know: - How to describe the effects of weak forces on molecular structure. o Strong acids dissolve completely o Weak acids do not fully dissolve Proteins and nucleic acids can dissolve due to hydrogen bonding H bonds between peptide groups and commentary bases of DNA Weak hydrogen bonds in proteins Hydrophobic substances
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Key force in protein stabilization Noncovalent bonds Important structural role - Henderson-Hasselbalch equation and how to use it. o ¿ A ¿ ¿ ¿ ¿ pH = p K a + log ¿ Buffering region pK a = pH ± 1 Chapter 3: Amino acids, etc. Important concepts: - Amino acids are the building blocks of proteins; they are also used as hormones and other signaling molecules. - Amino acids have acid-base properties. - Proteins can be separated by size, charge, hydrophobicity, affinity for a molecule, etc. - The sequence of a protein affects it physical and chemical properties. - Comparison of protein sequences can provide clues as to function (or at least what residues are important for structure & function). Know: - Amino acid structures, including pK a ’s. o Generic amino acid: + H 3 N CH C R O - O Amino group pK a = 9.5 Carboxylic group pK a = 2 o ***21 side chains Nonpolar: Gly- G, Leu- L, Val- V, Ala- A, Iso- I, Met- M, Pro- P Aromatic: F- Phe, Tyr- Y, Trp- W Tyr- Y: pK a = 10.1 Absorb ultraviolet light Polar uncharged: Cys- C, Thr- T, Asn- N, Gln- Q, Ser- S Cys- C: pK a = 8.2 Charged: Asp- D: pK a = 3.6 Glu- E: pK a = 4.2 Lys- K: pK a = 10.5 Arg- R: pK a = 12.5 His- H: pK a = 6 - Be able to calculate pI for a peptide, charge at a given pH. o Positive to negative - Major methods of protein purification (chromatography, electrophoresis). o Chromatography: analytical or preparative Molecule of interest has some differential affinity for solid phase vs. mobile phase Ion exchange : Named for what binds
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Proteins move through the column at rates determined by their net charge at the pH being used Cation exchange = negative beads, positively charged molecules o
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