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