Term
| Ethanol is converted to _______, by _________, generating ________. |
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Definition
| Acetaldehyde, by alcohol dehydrogenase, generating NADH |
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Term
| Acetaldehyde is converted to _______ by _________, generating ________. |
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Definition
| Acetate, by acetaldehyde dehydrogenase, generating NADH |
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Term
| What does disulfaram inhibit, what are the clinical consequences and clincial uses? |
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Definition
| Inhibits acetaldehyde dehydrogenase, leading to the accumulation of acetaldehyde and "hangover" effects. Used for alcoholics trying to quit |
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Term
| How does alcohol produce hypoglycemia and lead to hepatic steatosis? |
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Definition
| Creation of NADH shunts pyruvate and oxaloacetate away from gluconeogenesis, and towards production of lactate and malate. ie towards fatty acid synthesis |
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Term
| Kwashiorkor: Def, clinical picture |
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Definition
Protein malnutrition leading to skin lesions, edema, anemia, and liver malfunction due to fatty change.
Clinical picture: Small child with swollen belly |
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Term
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Definition
| Energy malnutrition leading to tissue and muscle wasting, loss of subcutaneous fat, and variable edema |
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Term
| What histones form nucleosome core, how many of each? |
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Definition
| 2 each of the positively charged H2A, H2B, H3 and H4 |
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Term
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Definition
| Ties nucleosomes together in a string (30nm fiber). Linker. |
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Term
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Definition
| DNA and histones in condensed, transcriptionally inactive form |
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Term
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Definition
| DNA and histones in less condensed, transcriptionally active form |
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Term
| Name the purines, how many rings? |
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Definition
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Term
| Name the pyrimidines, how many rings? |
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Definition
| Cytosine, thymine, uracil: one ring |
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Term
| Which nucleotide has a ketone, which a methyl group? |
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Definition
Guanine:ketone
Thymine: methyl |
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Term
| How do you make uracil, where is it found? What does it replace? |
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Definition
| Deamination of cytosine makes uracil, found in RNA instead of thymine |
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Term
| What are the nucleotide bonds in DNA? Which is stronger? Why? Consequence? |
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Definition
| A-T, G-C. The G-C bond is stronger b/c it has 3H-bonds, and A-T only has 2 H-bonds, Consequently, the more G-C links in DNA, the higher the melting point. |
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Term
| What are the amino acids necessary for purine synthesis? |
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Definition
Glycine
Aspartate
Glutamine |
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Term
| What are the amino acids necessary for pyrmidine synthesis? |
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Definition
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Term
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Definition
| Substituting purine for purine or pyrimidine for pyrimidine |
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Term
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Definition
| Substitution of pyrimidine for purine or vice versa |
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Term
| Components of a nucleotide, how are they linked |
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Definition
| Base + Ribose + phosphate, linked by a 3'-5' phosphodiester bond |
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Term
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Definition
| Each codon specifies only one amino acid |
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Term
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Definition
| More than one codon may code for the same amino acid |
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Term
| Commaless, nonoverlapping |
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Definition
| Read from a fixed starting point as a continous sequence of bases |
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Term
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Definition
| Genetic code is conserved throughout evolution |
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Term
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Definition
| Encoded by only one codon |
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Term
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Definition
| Same aa still coded for, often due to a base change in 3rd position of codon: termed tRNA wobble, tRNA can bind with different aa's in last position |
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Term
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Definition
| AA is changed, a conservative missense is a substitution for a new aa with similar chemical structure |
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Term
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Definition
| Change results in early stop codon, more severe than missense and silent |
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Term
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Definition
| Change resulting in misreading of all nucleotides downstream, usually resulting in a truncated protein |
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Term
| Eukaryotic Replication: Where does it start? How many origins? |
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Definition
| Eukaryotic replication begins at a consequence sequence of AT rich base pairs at multiple origins of replication |
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Term
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Definition
| Starts at a single origin of replication, with continuous bidirectional DNA sythesis on leading strand and discontinuous (Okazaki fragements) on lagging strand |
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Term
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Definition
| Enzymes that separate the parental strands of DNA, binding to single stranded DNA and racheting along in one direction, with each step hydrolyzing one ATP |
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Term
| Single stranded DNA binding proteins (SSBs) |
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Definition
| Prevent DNA from reannealing: keep the strands apart, reduce potential secondary structure formation, ie hairpins, and align template strands for rapid DNA sythesis |
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Term
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Definition
| Create a nick in the helix to prevent supercoils |
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Term
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Definition
| Makes initial primer composed of ribonucleotides providein a free 3' hyroxyl group on which DNA polymerase III can initiate replication |
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Term
| DNA polymerase III: Synthesis and proofreading |
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Definition
Elongates the chain by adding deoxynucleotides to the 3' end on the leading, continuous strand. Does the sam on the lagging strand at multiple sites.
Proofreads: 3'-5' exonuclease activity proofreads each added nucleotide |
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Term
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Definition
| Degrades the original RNA primers and fills the gap with DNA |
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Term
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Definition
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Term
| Semiconservative Replication |
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Definition
| Parent strand is 1/2 of new strand |
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Term
| Nucleotide excision repair |
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Definition
| ssDNA repair of DAMAGED DNA. Specific endonuclease enzyme complexes cut several NTs away on both sides of the damaged base, releasing an oligonucleotide containing damaged bases; DNA polymerase and ligase fill and reseal the gap. |
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Term
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Definition
| ssDNA repair of DAMAGED DNA. Specific glycosylases recognize and remove damaged bases, AP endonuclease cuts DNA at 5' apyrimidinic sites, but leaves sugar attached, AP lyase cuts 3' end and removes sugar. The empty sugar is removed, and the gap filled by DNA polymerase III and sealed by ligase. |
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Term
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Definition
| ssDNA repair of mismatched NTs due to ERRORS in replication, not damage. Unmethylated, thus newly synthesized string, is recognized, so that the correct genetic info is preserved. Mismatched NTs are removed, and the gap is filled/resealed. |
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Term
| Nonhomologous end joining |
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Definition
| dsDNA repair, bringing 2 ends of DNA fragments together, with no requirment for homology, can also lead to chromosomal translocations or the insertion of a DNA fragment anywhere into the genome |
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Term
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Definition
| Mutation in nucleotide excision repair leading to dry skin with melanoma and other cancers |
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Term
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Definition
| Mutation in mismatch repair system |
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Term
| Major result of UV damage |
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Definition
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Term
| DNA synthesis, RNA synthesis all proceed __________. |
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Definition
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Term
| 5' end contains ____________ which is the _________- |
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Definition
| the triphosphate, serves as the energy source for the bond. |
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Term
| How are amino acids linked? |
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Definition
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Term
| What is the largest type of RNA? |
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Definition
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Term
| What is the most abundant type of RNA? |
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Definition
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Term
| What is the smallest type of RNA |
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Definition
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Term
| Name the enzyme that makes each type of RNA in eukaryotes |
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Definition
RNA polymerase I makes rRNA
RNA polymerase II makes mRNA
RNA polymerase III makes tRNA |
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Term
| What enzyme makes each type of RNA in prokaryotes? |
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Definition
| RNA polymerase (multiunit complex) makes all 3 types of prokaryotic RNA |
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Term
| What inhibits RNA polymerase II, where is it found? |
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Definition
| alpha-amantin, found in death cap mushrooms |
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Term
| Special funtions of RNA polymerases |
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Definition
| No proofreading, but can initiate chains |
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Term
| How is DNA "opened" for transcription? |
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Definition
| RNA polymerase II opens DNA at promoter site |
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Term
| Start codon: definition, nucleotide sequence, codes for what in euks? what in prok? |
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Definition
Start codons are the site of mRNA initiation.
AUG (rarely GUG)
Euks: AUG codes for methionine (may be removed before translation finishes)
Prok: AUG codes for formyl-methionine (f-MET). |
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Term
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Definition
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Term
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Definition
| Site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus. (AT rich upstream sequence with TATA and CAAT boxes) |
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Term
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Definition
| Stretch of DNA that alters gene expression by binding transcription factors. May be located close to, far from, or even within an intron of the gene whose expression it regulates. |
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Term
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Definition
| Site where negative regulators, repressors, bind |
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Term
| Promoter mutations result in |
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Definition
| A dramatic decrease in the amount of gene transcribed |
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Term
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Definition
| INtervening noncoding segments of DNA remaining IN the nucleus |
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Term
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Definition
| The segments of DNA containing the actual genetic information that codes for a protein. |
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Term
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Definition
| Combining different exons to make unique proteins in different tissues |
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Term
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Definition
1) Primary transcript containing exons and introns combines with snRNPs to form spliceosome
2) Lariat shaped intermediate is generated with snRNP bringing GU of intron close to an A. The G and A combine. and form a loop, bringing exon1 and exon2 close
3) Lariate released to remove intron and precisely join 2 exons |
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Term
| What does snRNP look for? |
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Definition
| A GU after exon 1, an AG before exon2 |
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Term
RNA processing:
Site
When?
3 types
Consequence |
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Definition
Occurs in the nucleus after transcription:
1) 5' cap is added made of 7-methyl-G
2) 3' end is polyadenylated (approx 200 A's)
3. Introns are spliced out
Once processed RNA, is transported out of the nucleus |
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Term
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Definition
Heterogenous nuclear RNA; initial transcript.
mRNA: capped and tailed transcript |
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Term
| Aminoacyl-tRNA synthetase |
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Definition
| One per aa. It scrutinizes aa before and after it binds to tRNA. If its the wrong aa, it hydolyzes the bond. |
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Term
| Where does the energy for formation of the peptide bond come from? |
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Definition
| The aa-tRNA bond has energy for the peptide bond |
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Term
| Where/how is aa bound to tRNA? |
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Definition
| The aa is covalently bound to the 3' end of the tRNA |
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Term
| What do all tRNAs(euk and prok) have at 3' end? |
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Definition
| CCA at 3' end along with a high percentage of chemically modified bases |
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Term
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Definition
| Opposite 3'aminoacyl end in tRNA, binds to the codon for tRNA attachment |
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Term
| Describe structure of tRNA |
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Definition
| 75-90NTs, cloverleaf form, anticodon end opposite 3' aminoacyl end |
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Term
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Definition
| Accurate base pairing needed only in first 2 NT positions of an mRNA codon, so codons differing in the 3rd wobble position may code for the same tRNA/amino acid |
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Term
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Definition
| Where the incoming tRNA binds |
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Term
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Definition
| Accomodates the growing peptide chain. The tRNA holding it is the one that previously occupied the A site |
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Term
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Definition
| Holds the empty tRNA as it exits |
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Term
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Definition
| Initiation factors (IF), assemble the 40S ribosomal subunit along with the initiator tRNA, and are released when the mRNA and the ribosomal subunit assemble within the complex |
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Term
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Definition
1) Aminoacyl tRNA binds to A site
2) Peptidyltransferase catalyzes peptide bond formation, and transfers growing PP to amino acid in A site: requires GTP
3) Ribosome advances 3 NTs toward 3' end of RNA, moving peptidyl RNA to P site. |
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Term
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Definition
| Completed protein is released from ribosome, which dissociates |
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Term
| What step of protein synthesis requires ATP? |
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Definition
| tRNA Activation: charging it with aa |
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Term
| What step of protein synthesis requires GTP? |
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Definition
| tRNA gripping and moving: Translocation |
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Term
| Posttranslational Modifications |
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Definition
Trimming: Removal of N- or C- terminal propeptides from zymogens to create mature proteins
Covalent alterations: Phosphorylation, glycosylation, hydroxylation
Proteasomal Degradation: Attachment of ubiquitin to defective proteins to tag them for breakdown |
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