Term
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Definition
The building blocks that polymerize to form proteins. There are 20 AAs, each one with a unique side chain with specific biochemical properties.
Can be grouped by polarity:
-Nonpolar
-Uncharged polar
-Negatively charged polar
-Positively charged polar |
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Term
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Definition
| Proteins have sections with different chemical properties depending on the side chains of the amino acids in that domain. Some domains may be hydrophobic, to sit in the cell membrane, and some may be hydrophobic for exposure to extracellular fluid. |
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Term
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Definition
| Stereospecific enzymes synthesize amino acids so that they will have L-stereochemistry. Each AA consists of an asymmetric C atom attached to a carboxyl group, an amino group, a H atom, and the side chain (except for proline, which has a 5-C ring for a side chain that attaches to the amino group). |
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Term
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Definition
| AA carboxyls are ionized at pH 7, but the amino groups are not. This ionization can switch between the two groups at physiological pH meaning that AAs are zwitterions (molecules that can be completely positively or negatively charged at a given pH). pK values for each AA determine what pH they will be positively or negatively charged at. The pI value is the pH where the AA is neutral. This depends on the properties of the side chain. |
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Term
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Definition
Amino acids bind together when the amino terminal group attaches to the carboxyl terminal group of the next AA, forming a C-C-N substituted amide linkage (peptide bond). At one end of the polypeptide is the amino terminal end (NH2) and at the opposite is the carboxyl terminal end (COOH).
Peptide chains are synthesized from the amino to the carboxyl end. |
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Term
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Definition
All the proteins encoded in an individuals genome. Proteins are the most abundant macromolecules in the cell.
10x the size of the genome, for humans. |
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Term
| Primary Protein Structure |
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Definition
| The sequence of AAs read from the amino to the carboxyl end. A single AA substitution, addition, or deletion can drastically alter a protein's shape and function. |
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Term
| Secondary Protein Structure |
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Definition
| Amino acids in a protein can interact with each other to affect the protein's shape (beta-pleated sheets, alpha helices, random coils). |
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Term
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Definition
| Secondary structure found on DNA-binding proteins. Composed of 2 beta-pleated sheets, an alpha helix, and a stabilizing Zinc atom. |
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Term
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Definition
Secondary structure found on transcription proteins.
Have a conserved AA sequence with hydrophobic AAs every 7th AA, creating an outward radiating domain that can interact with other proteins. |
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Definition
| A secondary structure that binds to consensus DNA sequences (CANNTG). |
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Term
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Definition
| A secondary structure consisting of two alpha helices connected by a short AA chain. This fits into the major groove of DNA. |
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Term
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Definition
| The further folding of secondary structures to form the shape needed for protein function. Denatured proteins have lost their tertiary structure and therefore their functionality. A single AA change in the primary structure can mess up tertiary structure. |
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Term
| Quaternary Protein Structure |
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Definition
| Complexes (oligomers) of proteins (monomers) that perform a function together. |
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Term
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Definition
| Contain components other than AAs. Include lipoproteins, glycoproteins, and metalloproteins (e.g., hemoglobin). |
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Term
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Definition
Codons that terminate protein synthesis:
UAG
UAA
UGA
Start codon:
AUG |
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Term
| Amino Acid tRNA Synthesis |
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Definition
| 20 tRNA, one for each AA. Class I synthetases interact with the minor groove of the tRNA acceptor arm, and Class II with the major. Recognize AAs by side chain. Errant AAs bound to the wrong synthetase dissociate very quickly before charging occurs. If mischarging occurs, the wrongly charged tRNA will be hydrolyzed when it is released. Mischarging is 10^3-10^6 times less efficient than correct charging. |
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Term
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Definition
A 70s unit with a 30s small subunit and a 50s large subunit.
30s subunit
-16s rRNA
-21 ribosomal proteins
50s subunit
-5s rRNA
-23s rRNA
-34 ribosomal proteins |
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Term
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Definition
80s unit with a 40s small subunit and a 60s large subunit.
40s small subunit
-18s rRNA
-30 ribosomal proteins
60s large subunit
-5s rRNA
-5.8s rRNA
-28s rRNA
-40 ribosomal proteins |
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Term
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Definition
| Starts with methionine/N-formylmethionine. Initiating factors (IF) differentiate between initial methionyl tRNAs and normal ones. The small ribosomal subunit binds to IF-3 and then the 5' end of the mRNA (ribosomal binding site) so that AUG is in the right place. IF-2 with GTP and tRNAmet joins, and then the large ribosomal subunit, hydrolyzing GTP to release GDP and IF-2, IF-3. In the initiating complex, tRNAmet sits in the P site (all other tRNA bind to the A site). |
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Term
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Definition
Proteins that hold peptides in the process of being translated in a hydrophobic chamber. This lets nascent proteins start to fold and keeps them from binding to other nascent proteins. The chaperone attaches to the large ribosomal subunit.
DNaK protein from E. coli does this function by attaching to hydrophobic regions of the merging polypeptide. |
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Term
| tRNA Addition in Translation |
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Definition
The second tRNA-AA binds to the ribosomal A site along with the elongation factor Tu (EFTU) and GTP. The tRNA must be recognized and then proofread with hydrolysis of GTP by EFTU happening between the two. EFTU-GTP is released and converted to EFU-GDP by EF-T.
The first two codon-anticodon pairings are strictly proofread and the third less so, leading to "wobble". |
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Term
| Peptide Bond Formation in Translation |
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Definition
| The initial N-formylmthionyl-tRNA in the P site is transferred to the second tRNA-AA in the A site. A peptide bond is formed by peptidyl transferase, and RNA-mediated reaction (no proteins around). The ribosome moves so that the dipeptidyl-tRNA moves to the P, the empty tRNA is released into E. EF-G helps the tRNA move 20 A from the A to P and 28 A from P to E. The ribosome continues to move along and the peptide chain is attached to incoming tRNAs. Two GTP are used for each addition. |
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Term
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Definition
| When the ribosome reaches a stop codon, release factors (R1, R2, S in E. coli) hydrolyze the peptide from tRNA, release the tRNA from the ribosome, and dissociate the ribosomal subunits. eRF1 and eRF3 mediate the hydrolysis of the polypeptide in eukaryotes. |
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Term
| Translation in the Nucleus |
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Definition
| Most translation happens in the cytoplasm. Some might happen in the nucleus, based on the presence of translation factors in the nucleus and the fact that isolated nuclei will incorporate AAs into proteins. mRNAs with premature stop codons will be degraded in mammalian nuclei (nonsense-mediated decay). Nuclear translation might occur simultaneously with transcription, as it does in eukaryotes. |
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