Biol121 Midterm 2 Lecture 9-W 2025

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Nucleic Acid

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DNA/RNA

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Central Dogma

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DNA -> RNA -> Protein

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27 Terms

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Nucleic Acid

DNA/RNA

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Central Dogma

DNA -> RNA -> Protein

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Transcription

synthesis of an RNA molecule from a DNA template, first step of gene expression

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RNA polymerase

RNA synthesis

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sigma factor (sigma 70), "The housekeeping sigma factor"

recognizes promoter at -10 to -35 region, guides core enzyme to initiate transcription, responsible for transcribing most genes in bacteria like E. Coli

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Holoenzyme

Core enzyme + sigma factor

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Consensus sequences of sigma 70

TTGAT TATT

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Other sigma factors

Operate under variable conditions, perform same job as sigma 70.

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Sigma factor binding step 1

1) Bind to DNA

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Sigma factor binding step 2

2) Recruits core enzyme, scans for promoter

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Sigma factor binding step 3

3) Unwinds DNA at promoter

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Sigma factor binding step 4

4) Sigma factor released

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Direction and explanation of RNA synthesis

5' to 3', bases complementary to DNA template, has the same sequence as non template, but with U's instead of T's

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Rho-dependent transcription termination

Rho factor binds to mRNA, acts as a helicase, breaks off polymerase and mRNA off of DNA-> offers more precise control over termination

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Rho-independent transcription termination

polymerase slows at pause site, GC Rich sequence forms hairpin loop on mRNA, U-A base pairs located downstream of pause site, very unstable, polymerase released, mRNA breaks off DNA

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mRNA

tRNA

rRNA

sRNA

messenger RNA transfer RNA--> carries information from DNA to protein

Ribosomal RNA(Structural, non coding)

Small RNA-->postranscriptional regulation of specific Mrna into protein

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Translation

Decoding of RNA to protein

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The Genetic code is degenerate

• There are 64 codons, but only 20 amino acids, multiple codons can code for the same amino acid

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Open Reading Frame(ORF)

Each codon has three different possible reading frames, Reading can start at the first, second or third nucleotide of the RNA. Stop codon is in the same reading frame as the start codon

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transfer RNA

binds individual amino acids--> have 3 base anticodon, base pair to codons in mRNA,

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aminoacyl tRNA transferases

Attach amino acid to tRNA-->"Charge the tRNA

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Ribosomes

2 subunit composition--> 30S(small), 50S(big) , bind 1 mRNA and 3 tRNA

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Transcription and Translation in Prokaryotes

Both are coupled, nothing separating the two processes. Ribosomes bind mRNa while mRNA still being synthesized, multiple ribosomes can bind to mRNA--> super fast protein synthesis

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Ribosome sites

A site: binds free Aminoacyl- tRNA

P Site: binds Peptidyl-tRNA

E Site: Exit site,

(Not really talked about this in depth in class)

<p>A site: binds free Aminoacyl- tRNA</p><p>P Site: binds Peptidyl-tRNA</p><p>E Site: Exit site,</p><p>(Not really talked about this in depth in class)</p>
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translation intiation

Shine-Dalgarno sequence on mRNA, ALLOWS binding to 30S subunit., IF3 DOES the actual binding, IF1 blocks A site, IF2 brings in formylmethionine for start codon-Formyl, specific to bacteria, first codon tRNA binds directly to P site.

Way to remember what IF1 and IF2 do-->

- First site of ribosome is A site, we can call this site 1, therefore IF1 acts on site 1

-IF2 acts on site 2(P site), bringing in formylmethionine.

Think since the exam is multiple choice this might help even if you forget specifically what IF1 and IF2 actually do.

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Translation elongation

1) Aminoacyl trna binds to A site

2)Peptide bond formed between new amino acid and growing peptide chain in P site

3) Ribosome shifts mRNA one codon

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Translation Termination

Stop codon on mRNA enters A site, Protein release factor enters A site(NO trna), peptidyl transferase activated, releases completed proteins, Ribosome recycling factor enters A site and ribosome falls apart.