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MMBio Quiz 2
| Term | Definition |
|---|---|
| amino acids (4 parts) | alpha carbon (center) carboxyl group - COO- hydrogen R group/side chain amino group - NH3 |
| basic amino acids | positively charged highly polar |
| acidic amino acids | negatively charged with carboxyl group highly polar |
| uncharged polar amino acids | uncharged but polar R groups |
| hydrophilic amino acids: | acidic, basic, and uncharged polar |
| hydrophobic amino acids | nonpolar R groups are hydrocarbon chains and rings |
| 5 to 3 N to ... | C |
| always add an amino acid to the ___ terminus | C |
| how a peptide bond is formed | C from carboxyl group attaches to the N in the NH3, H2O is lost |
| a peptide bond is a | C-N bond, covalent bond |
| methionine | first amino acid in a sequence, AUG "start" codon |
| cysteine | only amino acid that can form disulfide bonds only R group that can covalently bond with another stabilizes protein folding |
| amino acids with hydroxyl group (OH) | common target for addition for other molecules |
| some proteins will fold to the correct shape on their own, others require ______ _______ to help correct and assume the correct shape | chaperone proteins |
| chromatography | process to purify molecules from a mixture |
| column chromatography | method used to separate molecules (like a protein) from one other |
| columns contain beads which | are packing material, allows specificity of what you want to purify |
| you can elute columns | which adds liquids, slowly drip out through gravity, the right type is released |
| at the end you catch the | fraction |
| ion exchange chromatography | separation by charge pack bead of opposite charge that you want, your proteins stick, others fall out |
| if you have a higher salt concentration in the ion exchange column you can better distinguish between | highly and lowly charged |
| reverse phase chromatography | separation by hydrophobicity beads are hydrophobic, hydrophobic proteins stick |
| if you have lower salt concentration in the reverse phase column you can better distinguish | low hydrophobicity comes off first, high hydrophobicity last |
| gel filtration chromatography | separation by size large proteins pass through column first because smaller proteins get trapped in sieve/pores of beads |
| affinity chromatography | separation by shape (specific interactions with something on the beads) |
| you should use multiple types of tests of chromatography to ensure you get your | final, purified, desired, correct protein |
| protein folding | transition from stick-figure of amino acids to a 3D shape |
| proteins do nearly everything for a cell | synthesizing, communication, destruction (not genetic material) |
| protein folding is usually _____ and occurs ______ | spontaneous, naturally |
| primary structure | linear sequence of amino acid structure peptide bonds |
| secondary structure | folding of backbone H-bonds in backbone |
| two types of secondary structures | alpha-helix - interactions with proximal amino acids beta-sheets - interactions with distant amino acids |
| loops in beta sheets | region or poorly defined structure in between alpha and beta |
| tertiary structure | 3D shape of single polypeptide chain interactions between R groups/side chains multiple alpha and beta |
| what stabilizes tertiary structures | H-bonds hydrophobic bonds ionic bonds disulfide bonds |
| quaternary structures | multiple polypeptide chains stabilized by same as tertiary (H, ionic, hydrophobic, and disulfide bonds) |
| anti-parallel beta-sheets | N-terminus lines up with C-terminus of another |
| phosphate group is _____ charged | negatively |
| DNA backbone is | negative (because of phosphate) and is made of the sugar and the phosphate |
| DNA polymerase can only form a bond using a | free 3' OH group |
| A-T can only form 2 H-bonds because the C | is not an acceptor, and can't hydrogen bond |
| base attachment to sugar is off-center which causes a geometry issue and forms | grooves |
| the open grooves exposes more chemical info and allow for | transcription factors to better read and bind |
| R cells were non-virulent and S cells were | virulent |
| Griffith's experiment proved | something from the dead S-cells was transferred into the R cells but he didn't know what |
| Chargaff proved | specific base pairing |
| P32 on DNA stayed in the _____ and S35 and protein was outside in the ______ (after centrifugation) | P32/DNA - pellet S35/protein - supernatant |
| polar but uncharged amino acids are often on | protein surface (touching water, forming H-bonds) |
| nonpolar amino acids are often | buried inside proteins, away from water |
| peptide vs polypeptide | peptide - short chain polypeptide - long chain |
| forming a peptide bond releases | water so the C and N can bond without the H H and O |
| chaperone proteins aren't part of the protein, they just | assist |
| ion chromatography | separates by charge |
| reverse phase chromatography | separates by hydrophobicity |
| gel filtration chromatography | separates by size |
| affinity chromatography separates | binding/shape |
| primary | sequence of amino acids peptide bonds |
| secondary | local shapes H-bonds in backbone |
| tertiary | 3D shape R-group interactions |
| quaternary | multiple chains - proteins all bonds |
| histone | protein that pulls DNA together |
| DNA wraps around histone octamer to form a | nucleosome |
| nucleosome is so that | DNA is compact and organized |
| chloroform | improves phenol separation by making layers more distinct |
| alcohol precipitiation | makes DNA clump and come out cold |
| mass ladder works as a | ruler/comparison/control |
| BME | breaks S-S bonds and makes proteins linear (denatures) |
| example of restriction enzyme | EcoR1 only cuts at GAATTC |
| primers tell you where to | start copying |
Created by:
anyasalmon