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Bio 3 exam
| Term | Definition |
|---|---|
| Gene | region of DNA encoding a single polypeptide OR encoding an RNA with a function (rRNA, tRNA, small noncoding RNAs) |
| Transcription | polymerization of NTPs in 5’ -> 3’ direction catalyzed by RNA pol. Process that builds mRNA using DNA within a gene. |
| Template strand | DNA strand that is copied by RNA polymerase |
| Coding strand | Not copied and RNA molecules have the same sequences as it |
| Transcription start site (TSS) | where RNA polymerase actually begins transcription |
| Promoter (Upstream): | DNA sequence that determines if and where RNA pol will start transcription |
| Transcription factors | proteins that bind to DNA to regulate transcription and recruit RNA polymerase |
| Why would a cell bother to transcribe DNA into RNA? | Amplification, regulation, evolution (RNA likely came first), and protection of DNA in the nucleus |
| RNA pol I: | Transcribes rRNA and some small RNAs |
| RNA pol II: | Transcribes mRNA and some small RNAs |
| RNA pol III: | Transcribes tRNA and some small RNAs |
| Basal txn factors for RNA pol II | TATA-binding proteins bind to the sequence and then TBP-associated factors bind to the TBPs |
| To begin transcription | kinase bound to txn factor activity phosphorylates specific amino acids in C-terminal domain (CTD) of RNA pol II |
| RNA pol II comes off | Conserved DNA sequence) that recruits proteins that modify the 3’ end of the new mRNA |
| mRNA processing | 5’ capping, 3’ polyadenylation, splicing (pre-mRNA to mature mRNA) |
| 5’ cap: | Guanine gets attached to 5’ end of pre-mRNA -> 5’ carbon of G gets linked to 5’ carbon of 1st nucleotide in mRNA → - Methyl groups are attached to nucleotides |
| 5' cap and 3’ polyadenylation helps with: | Protects mRNa from degradation by enzymes, Recognized by other proteins for transport out of nucleus, Recognized by proteins that help the mRNA associate with ribosomes |
| 3’ polyadenylation | ~30 – 250+ ‘A’ nucleotides are attached to 3’ end of RNA – added by a complex of proteins that recognize “AAUAAA’ sequence, cut the mRNA, and recruit PolyA-polymerase |
| RNA splicing: | put together exons, remove introns |
| Process of RNA splicing: | snRNPs recognize specific sequences in pre-mRNA at splice sites, forming a spliceosome complex with the mRNA |
| Central Dogma | DNA-DNA (replication) DNA-RNA (Transcription) RNA- Protein (Translation) |
| mRNA | acts as a messenger carrying DNA encoded info and is translated into a protein. |
| rRNA | forms part of the structure of ribosomes |
| tRNA | carries amino acids to the ribosome during translation and contains anti- codons (3 nucleotides complementary to the mRNA codons) |
| One snRNP creates 5’ splice site | attaches 5’ end of intron to an ‘A’ nucleotide near 3’ end of intron, forming a lariat structure Then creates 3’ splice site, and lariat structure is released- – phosphodiester bond between exons |
| How does mRNA encode for proteins? | codons that are non-overlapping and have a wobble! |
| ORF | Open reading frame. Starts at AUG and ends at first in frame stop codon (UAA, UAG, or UGA) |
| Point mutation | Missense mutation: nucleotide change causes change in a.a sequence. ex. UAC (Tyr) - UGC (Lys) |
| Silent Mutation | nucleotide change does not create change in a.a sequence. ex. UAC (Tyr)- UAU (Tyr) |
| Nonsense Mutation | nucleotide change causes an early stop codon. ex. UAC (Tyr)- UAG (stop) |
| Frameshift Mutation | addition or deletion of nucleotide that causes shift in reading frame. ex. UAC UAC UAC (Tyr-Tyr_Tyr) to UAC GUAC UAC (Tyr- Val-Leu) |
| The machinery of translation | ribosome (small and large subunit) and tRNAs |
| Ribosome has EPA sites reads from | reads from 3’ to 5’ |
| Epigenetics | non-nucleotide based information in the genome that exerts regulatory control over gene expression. |
| Nucleosome | DNA wrapped around histones |
| Acetylation | makes histones more open/ opens up the chromatin |
| Methylation | turns off genes, especially when promoter is methylated (looks packed) |
| HAT | does acetylation |
| HDAC | condenses it again |
| Why do cells regulate gene expression? | 1. cells differentiate. 2. conserve energy. 3. adapt |
| DNA sequences regulating transcription: | promoter-proximal elements, enhancer, silencer - activators or repressors bind |
| Promoter-proximal elements (PPE) | near promoter, not required, can increase or decrease txn, proteins: activators or repressors |
| reporter sequences | a way to study gene regulation sequences that are important for transcription |
| Enhancers | far away (both up and down stream), not required, increases txn, proteins activators |
| Silencers | far away, not required for txn, decreases txn, proteins: repressors |
| Reporter assays | promoter or regulatory sequence is placed near a reporter gene and the amount of txn is measured. |
| RISC (RNA induced silencing complex) | Small RNA binds mRNA target, Protein cuts mRNA target |
| Post-translational Modifications (PTMS) | Covalent modifications to amino acid. Phosphorylation and Ubiquitination |
| Phosphorylation | adds neg. phosphate to ser, thr, tyr often activates a protein |
| Ubiquitination | covalent attachment of ubiquitin to a protein , cuts up a protein |
| Heterochromatin | Tight packed and low transcription activity |
| Euchromatin | Loosely packed and high transcription activity |
| Histone acetylation | loosens the chromatin structure, making the DNA accessible to RNA polymerase |
| TATA box | sequence of repeated AT located in the promoter that recruits the TIC (transcription initiation complex). |
| RNAi | RNA interference process of small noncoding RNAs blocking translation of target mRNA molecules. |
| Small noncoding RNA | short strands of RNA that have a complementary sequence to their mRNA target. |
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