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PDBio midterm 2
transcription, translation, replication, DNA, RNA
| Question | Answer |
|---|---|
| Define the Oparin-Haldane proposal | chemical evolution- chemical reactions in the atmosphere and ocean of ancient Earth led to the formation of the first complex carbon-containing compounds (3-38) |
| name the two components of a scientific theory | 1. a statement about a pattern that exists in the matural world 2. a proposed mechanism or process that explains the pattern |
| define the prebiotic soup | amino acids, nucleotides, and sugars accumulating in the ancient ocean |
| the question of Stanley Miller's experiment | can complex organic compounds be synthesized from the simple molecules present in Earth's early atmosphere and ocean; is it possible to re-create the first steps in chemical evolution by simulating ancient Earth condition in the laboratory? |
| Describe Miller's Spark-Discharge Experiment | he had a mini ocean of H2O and an atmosphere of CH4, NH3, H2 connected by glass tubes. the water was constantly boiling and he sent mini lightning bolts through the atmosphere |
| The conclusion of Miller's experiment | the sparks and heating led to the synthesis of compounds that are the building blocks of proteins: amino acids. |
| Amino Acids | the 20 building blocks of proteins |
| The structure of Amino acids | carbon atom bonded to... 1. NH2- the amino acid functional group 2.COOH- the carboxyl functional group 3. H- a hydrogen atom 4. an "R" group- an atom or group of atoms called a side chain |
| Amino Group | the NH2 of an amino acid. in water it acts as a base to form NH3+ |
| carboxyl group | the COOH of an amino acid. in water it acts as an acid to form COO- |
| the importance of the amino group and carboxyl group having a charge | 1. they help amino acids stay in solution where they can interact with one another and with other solutes 2. they alter amino acid chemical reactivity. |
| side chain | r-groups. vary for each amino acid. they can be a single H or a carboxyl group. the properties of amino acids vary because their R-groups vary |
| Amino acids with nonpolar side chains are... | hydrophobic- do not form bonds with water |
| Amino acids wtih polar or charger side chains are... | hydrophilic- dissolve easily in water |
| monomer | a molecular subunit- nuleotide, sugar, amino acid. put together= polymer |
| building blocks of a protein | amino acids |
| macromolecule | a very large molecule that is made up of smaller molecule joined together |
| polymerization | bonding together of monomers |
| condensation/ dehydration reactions | the process of monomers polymerizing. the newly formed bond results in the loss of a water molecule. |
| hydrolysis | breaks polymers apart by adding water molecule |
| Peptide Bond | the bond that forms between the carboxyl and amino group of two amino acids. it is a C-N bond that results from a condensation reaction. |
| polypeptide | a molecule resulting from a group of amino acids linking by peptide bonds into a chain. |
| R group orientation of a polypeptide | they poke out of the peptide-bonded backbone |
| directionality of a polypeptide | the left side of a polypeptide is N-terminum and the right side is C-terminus |
| N-terminus | the left side of a polypeptide. it is the side with a free amino group |
| C-Terminus | the right side of a polypeptide. it is the side with a free carboxyl group |
| Flexibility of a polypeptide | the single bonds on either side of a peptide bond are flexible but it is not |
| oligopeptide/ peptide | a polypeptide made up of less than 50 amino acids |
| protein | polypeptide containing 50+ amino acids |
| 6 functions of proteins | catalysis, defense, movement, signaling, structure, transport |
| primary structure of a protein | the unique sequence of amino acids in a protein |
| Secondary Structure of a protein` | distinctively shaped sections of proteins that are stabalized largely by hydrogen bonding that occurs between the carbonyl oxygen of one amino acid residue and the hydrogen of the amino group of another |
| the alpha helix secondary structure of a protein | the polypeptide's backbone is coiled |
| Beta-pleated sheet secondary structure of a protein | segments of a peptide chain bend 180 and then fold in the same plane |
| Tertiary structure of a protein | results from interactions between R-groups or between R-groups and the peptide backboen |
| 5 types of interactions involving side chains of proteins | hydrogen bonding, hydrophobic interactions, van der Waals interactions, covalent bonding, ionic bonding |
| hydrogen bonding | form between hydrogen atoms and the carbonyl froup int eh peptide-bonded backbone, and between hydrogen and atoms with partial negative charges in side chains |
| Hydrophobic interactions | the hydrophilic side chains interact with water, causing the hydrophobic side chains to form globular masses |
| van der Waals interactions | once the hydrophobic side chains are closer together, they are stabalized by electrical attractions known as van der Waal interactions. the bonds are weak, but a lot of them increases stability |
| covalent bonding | form between sulfur atoms when a reaction occurs betweent eh sulfur-containing R-groups of two cystines. they create strong links between distinct regions of the same polypeptide |
| ionic bonding | these bonds form between side groups with full and opposite charges |
| Quaternary structure | the combination of polypeptide subunits |
| multienzyme complex | a group of enzymes,e ach of which catalyzes one reaction, that are physically joined together. |
| denatured | protein is unfolded |
| Molecular Chaperones | folding of proteins is often facilitated by specific proteins |
| prions | improperly folded proteins that act as infectious disease-causing agents |
| substrates | reactant molecules |
| catalyst | a substance that lowers the activation evergy of a reaction and increases the rate of the reaction. the composition of the catalyst is the same before and after the reaction. it only changes the free energy of a reaction!!! |
| enzyme's active site | the location where substrates bind and react on an enzyme |
| induced fit | enzymes undergo significant change in shape, or conformation, when reactant molecules bind to the active site |
| enzyme cofactors | atoms or molecules that are not part of the enzyme;s primary structure and often required to help the enzyme function. metal ions or small, organic molecules called coenzymes |
| competitive inhibition | a molecule similar in size to the substrate binds to the active site |
| allosteric regulation | molecules bind at a location other than the active site |
| nucleic acids | polymers made up of nucleotides |
| three components of a nulceotide | phosphate group, sugar, nitrogenous base |
| a sugar (in terms of nucleic acids) | an organic compound with a carbonyl group and several hydroxyl groups |
| pyrimidines | C, T, U |
| purines | A, G |
| phosphodiester linkage | joins the 5' carbon of a ribose of one nucleotide to the 3' carbon of another |
| phosphorylated | polymerzation can take place in a cell when the free energy of teh nucleotide monomers is first raised by reactions that add two phosphate groups to the ribonucleotides or deoxys, |
| antiparallel | two stands of DNA together, one running 5-3 and the other 3-5 |
| complementary base pairing | AT and GC |
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