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.