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Biochemistry
Week 1 - 6 (not aa)
| Question | Answer |
|---|---|
| What are 5 characteristics of organic compounds? | 1. Contains carbon 2. Covalent bonds 3. Low melting point 4. Low boiling point 5. Flammable |
| What type of bonds do alkanes have? | Single |
| What type of bonds do alkenes have? | Double |
| What type of bonds do alkynes have? | Triple |
| Root for 1 carbon | Meth- |
| Root for 2 carbons | Eth- |
| Root for 3 carbons | Prop- |
| Root for 4 carbons | But- |
| Root for 5 carbons | Pent- |
| Root for 6 carbons | Hex- |
| Root for 7 carbons | Hept- |
| Root for 8 carbons | Oct- |
| Root for 9 carbons | Non- |
| Root for 10 carbons | Dec- |
| What is a carboxyl group (COOH)? | Carbonyl (double bond O) + Hydroxyl groups (COH) |
| What is the suffix for carboxilic acids? | -oic acid |
| What is an aromatic amine called? | Aniline |
| How do you name amines? | Alkyl group followed by -amine. |
| What makes up "the matrix of life"? | Carbon and Hydrogen |
| What molecule provides energy? | Carbon |
| What are the 4 major classes of macromolecules? | 1. Proteins 2. Lipids 3. Nucleic Acids 4. Carbohydrates |
| What is the subunit for proteins? | Amino acids |
| What is the subunit for lipids? | Fatty acids and Glycerol |
| What is the subunit for carbohydrates? | Monosaccharides |
| What is the subunit of nucleic acids? | Nucleotides |
| What determines the function of a protein? | Its 3D structure |
| What determines the 3D structure of a protein? | Its sequence |
| Name the 2 Nucleic acids? | DNA and RNA |
| What is glycogen? | A long chain of glucose. |
| What is a special characteristic of lipids? | Their dual chemical nature. |
| What is the dual chemical nature? | Part hydrophobic and part hydrophilic. |
| What is the central dogma? | DNA transcribed to RNA translated to protein. |
| What is the initial place for protein synthesis and glucose metabolism? | Cytoplasm |
| What is the largest organelle? | Nucleus |
| What is the difference between prokaryotes and eukaryotes? | Eukaryotes have a nucleus |
| What is the cytoskeleton? | The organisation of the cytoplasm. |
| What organelle produces 90% of the energy in a cell? | Mitochondria. |
| How do you name binary acid (H + nonmetal)? | Hydro__ic acid |
| How do you name oxyacid w/ H and polyatomic ion? | From -ate to -ic acid |
| How do you name oxyacid w/ one less O than common form? | From -ite to -ous acid. |
| What are the Arrhenius properties of Acids and Bases? | Acids produce H+, Bases produce OH- |
| What are the Bronsted-Lowry properties of Acids and Bases? | Acids donate H+, Bases accept H+ |
| According to Bronsted-Lowry, what does an acid become once it gives away its H+? | Its conjugate base. |
| According to Bronsted-Lowry, what does an Base become once it accepts a H+? | Its conjugate acid. |
| [ H2O + CO3^2- -> HCO3- + OH- ] Find all the components in this reaction. | Acid : H2O conjugate base: OH- Base: CO3^2- Conjugate acid: HCO3- |
| What is the difference between a strong and a week acid-base? | Strong acid-base will dissociate completely while week ones dissociate only slightly. |
| What are strong bases made of? | Metals from group 1 and group 2. |
| What is the difference between Kc and Ka? | The Ka value doesn't include the concentration of the water. |
| What is the number of decimal places in the pH equal to? | The number of significant figures in the coefficient of [H3O+]. |
| Is Ka larger w/ a strong acid or with a week acid? | Strong acid |
| What is Kw? | The ion product constant for water. Kw = 1.0 x 10^-14 |
| What is the Brownian Motion? | The mouvement of particules due to random fluctuation of energy in the environment. |
| Hot does heat affect Brownian Motion? | Heat makes the particles go faster and cold makes them go slower. |
| What properties of water makes it perfect for life? (3) | 1. polarity 2. hydrogen bonding 3. Solvent properties |
| What is the universal solvent? | Water |
| Why is water a good solvent? | Because it is a dipole. It will dissolve any thing that has a charge on it. |
| What makes ice float? | The static bonds in ice are spread at max making its density smaller. |
| Explain van der Waals. | Slight polarity within the atom allows static attraction. |
| What is entropy? | The measure of randomness. |
| How is water entropy? | Really high. |
| What does hydrophobic means? | It won't dissolve in water. |
| What is the order of increasing bond strength? (7) | 1. Van der Waals 2. Hydrophobic 3. Hydrogen 4. Ionic 5. Single 6. Double 7. Triple |
| How does hydrophobic effect can influence protein folding? | Hydrophobic molecules will wrap themselves in not to be in contact with water. |
| What does it means when the pH of the solution is equal to the pKa of the weak acid? | Max buffer capacity |
| What is a titration? | An experiment in which you measure the amount of acid or base added to measured amount of base or acid. |
| What is the equivalence point? | The point in an acid-base titration where neutralization has been reached. |
| What are the 2 classes of proteins? | 1. Globular : Hydrophilic exterior 2. Fibrous : structural proteins |
| What is the entire protein complement of a cell called? | The proteome. |
| How do you determine the 3D structure of a protein? | X-ray crystallograpy |
| What are the 4 levels of protein structure? | 1. Primary : Sequence 2. Secondary : Hydrogen bonding 3. Tertiary :3D 4. Quaternary : subunits |
| How do you read a a.a. sequence? | From N-terminus to C-terminus |
| What is the molecular weight of a.a? | 110g/mol |
| What is the unit for the mass of proteins? | Daltons (KiloDaltons) |
| what is it called when 2 peptide chains are hooked to each other? | Crosslinked |
| What are the 2 predominant types of secondary structures? | 1. Alpha helices 2. Beta sheets |
| Where is the R group on an alpha helix? | Extending outwards |
| How are alpha helices stabilized? | Hydrogen bonds parallel to the helix. |
| what are the factors that can disrupt an alpha helix? (3) | 1. Presence of proline 2. Electrostatic repulsion 3. Steric crowding (proximity of bulky R groups) |
| How are beta sheets formed? | H-bonding between peptide bonds located across each other on opposite strands. |
| How are alpha helix formed? | H-bond between the C=O group of one a.a. and the N-H group of the a.a. that is 4 residues ahead of the chain. [n - n+4] |
| What are the 2 type of beta sheets? | Parallel and antiparallel |
| Which type of beta sheet is stronger? | Antiparallel |
| What are 2 supersecondary structures? | Coiled coil and triple helix |
| What are the different types of bonds in the tertiary structure? (4) | Ionic bond, disulfide bridge, hydrophobic interaction, hydrogen bond |
| What are independently folded compact units called in the tertiary structure? | Domains |
| what happens in the quaternary structure? | Association of 2+ polypeptide chains. creates dif. subunits. |
| Name 2 proteins with quaternary structure. | 1. Ribosome 2. Hemoglobin |
| What is a monomeric protein? | 1 polypeptide chain |
| What is a multimeric protein? | 2+ polypeptide chains |
| What dictates the function of a protein? | Its structure |
| What are 4 noncovalent interactions? | 1. H-bonding 2. Hydrophobic interaction 3. Electrostatic attraction 4. Electrostatic repulsion |
| What are molecular chaperones? | Heat shock proteins. They aid with protein folding and survival during times of stress. |
| What causes a proteome to vary? (3) | 1. Cell type 2. Dev. stage 3. Env. conditions |
| What are the 4 properties of proteins? | 1. Size 2. Net charge 3. Substrates 4. Solubility |
| What are the 4 basic steps of protein purification? | 1. Break open cell + Dif. centrifugation 2. Crude extract contains protein of interest 3. General protein separation 4. Specific protein separation |
| How does dif. centrifugation work? | Centrifuge at different speeds to extract dif sizes of particles. |
| What are 4 types of protein purification? | 1. Salting out 2. Gel-filtration 3. Ion-Exchange 4. Affinity Chomatography |
| How does salting out work? | Uses dialysis bag to separate according to solubility. |
| How does gel-filtration work? | Uses column with porous beads to separate according to size. Large molecules get down faster. |
| How does ion-exchange work? | Uses columns with charged beads to separate according to net charge. Same charge gets down faster. Uses salt to get opposite charge unbound. |
| How does affinity chromatography work? | Uses columns with beads with ligands to separate according to affinity. No affinity gets down faster. Uses salt to get ones with affinity. |
| Explain HPLC. | High Pressure Liquid Chromatography : Faster and better results. |
| How does gel electrophoresis (SDS-PAGE) work? | SDS makes protein linear and negatively charged. Electric currant separates according to size. No loading dye. Soak gel into dye afterwards. |
| What does SDS-PAGE stands for? | Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis. |
| How does Isoelectric focusing work? | Uses pH gradient to separate according to isoelectric point. |
| What is an isoelectric point? | Where the molecule has not charge. |
| How does 2D gel work? | Uses IEF and SDS-PAGE to separate according to size and charge. |
| How does Edman Degradation work? | Cleavage of a.a. from N-terminus. |
| How does Trysin enzyme work? | Cleavage at a.a. w/ +ve charge (H-R-K) |
| How does Chymotrypsin enzyme work? | Cleavage at aromatic a.a. (F-Y) |
| How does Cyanogen Bromide Chemical work? | Cleavage at Met. |
| How does Ultracentrifugation work? | 1 000 000 x g centrifugation separates fractions depending on sedimentation coefficient (mass, density, shape) |
| How does the Bradford assay work? | Coomassie Brilliant Blue dye is used to measure the [] of protein in a solution. (protein=blue) |
| Explain immunology. | 1. Ab is injected to rabbit 2. draw blood to separate serum 3. serum contains Ab to exposed antigen 4. hybridoma 5. Grow cell in vivo or in vitro |
| Define Hybridoma | Combine cell that produce Ab with immortal cell line (multiple myeloma) |
| How does immunoprecipitation work? | Chromatography with beads that attract antibody. |
| What does ELISA stand for? | Enzyme Linked Immunosorbant Assay |
| What are the 2 types of ELISA? | Indirect and sandwich |
| How does indirect ELISA work? | Sample added to antigen, serum washed out, antibody added to bind to specific antibody. If specific antibodythere, new antibody will bind to it an induce color change. =positive |
| Give an example of test that uses indirect ELISA. | HIV |
| How does sandwich ELISA work? | Sample added to antibody, serum washed out, antibody added to bind to specific antigen. If specific antigen there, antibody will bind to it and induce color change. = positive |
| Give an example of test that uses sandwich ELISA. | Pregnancy test |
| How does Western Blots work? | SDS-PAGE with polymer sheet on it. Expose sheet to antibody. Expose sheet to x-ray or UV to see band where antibody and protein bound. |
Created by:
kboivin
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