Transcription of DNA into RNA, enzymatic reactions, RNA, RNA degradation

  • Transcription
    1. Initiation: promoter recognition, closed complex, open complex.
      • Promoter:
        • Prokaryotic: ←upstream, -35 region, Pribnow box, transcription start site (TSS, +1), downstream→
        • Eukaryotic: ←upstream, several upstream elements, TATA box, initiator element containing TSS (+1), downstream→
        • The high A-T composition in promoters facilitate unwinding of DNA.
        • Template strand = antisense strand = (-) strand = noncoding strand = the DNA strand that serves as the template for transcription.
        • Nontemplate strand = sense strand = (+) strand = coding strand = the DNA strand having the same sequence as the transcribed RNA.
      • Binding to promoter:
        • Prokaryotic:
          • holoenzyme = core enzyme (polymerase activity) + σ-subunit (promoter and strand specificity).
          • binding first forms the closed complex, and then DNA opens up, forms the open complex.
        • Eukaryotic:
          • A whole bunch of transcription factors (TFs) involved in promoter recognition, binding, and openning up DNA.
          • TBP = Tata binding protein. TAF = TBP associated factor.
          • Phosphorylation of Pol II C-terminal domain (CTD) opens DNA up, forms the open complex.
        • Polymerase must transcribe using the correct template strand. The σ-factor (prokaryotes) and TFs (eukaryotes) tell the RNA polymerase to bind the coding strand, while using the template strand as the template.
    2. Elongation:
      • Polymerases:
        • Prokaryotes have just one.
        • Eukaryotes have three:
          • 1. RNA Pol I: makes rRNA (except the small 5S rRNA that resembles a tRNA in size).
          • 2. RNA Pol II: makes mRNA.
          • 3. RNA Pol III: makes tRNA (and 5S rRNA).
      • Incorporation of NTPs.
      • Prokaryotes lose σ-subunit. Eukaryotes lose TFs.
      • Topoisomerases relaxing supercoils ahead and behind the polymerase.
      • Transcription-coupled repair: RNA Pol II encounters DNA damage, backs up, TFIIH comes along, recruits repair enzymes. Defective TFIIH → faulty transcription-coupled repair → Xeroderma pigmentosum and Cockayne syndrome (skin sensitive to sunlight radiation in both diseases).
    3. Termination
      • Prokaryotic:
        • Intrinsic termination: GC hairpin (stalls polymerase) followed by poly U (slips off).
        • Rho-dependent termination: ρ protein catches up to polymerase when it stalls at the hairpin, and bumps it off.
      • Eukaryotic:
        • Termination consensus sequence reached (AAUAAA).
        • Polymerase released somewhere further downstream to the consensus sequence.
  • RNA
    • 1. RNA = ribonucleic acid, has 2’-OH.
    • 2. rRNA = ribosomal RNA
      • Most abundant (r for rampant).
      • Catalyzes peptide bond formation in the ribosome.
    • 3. mRNA = messenger RNA
      • Longest (m for massive).
      • Contains sequence of codons for translation.
      • RNA splicing
        • pre-mRNA need to be processed.
        • Introns = interfering sequences, cut out.
        • Exons = spliced together.
        • RNA splicing proceeds via a lariat intermediate, by the action of the spliceosome (snRNPs), introns released in lariat form.
        • Some RNA can self splice.
    • 4. tRNA = transfer RNA
      • Smallest (t for tiny).
      • Contains anticodon.
      • Shuttles the correct amino acid to the correct codon during translation.
    • 5. snRNPs (snurps) = RNA + protein, involved in RNA splicing.
  • RNA degradation
    • RNases degrade RNA.
    • Post-transcriptional modifications protect RNA from degradation (5’ cap and polyA tail)
    • 2’-O-methylation prevents that position from attacking the RNA backbone.
Study Session - Barry Imagine

Rating: … I guess PG-13… cuz Im pretty paranoid it is.

Warning: very very very awkward Barry, and just, and i really mean just a bit of stripping…

Summary: Christmas Break is amazing, but it also comes with the dreaded word, Midterms. You need to study Biology with Barry and your other classmates.

Word Count: (the longest imagine by far!) 1329

Christmas break was around the corner, and you were excited! However, before you get to the tree, lights, and cookies, you have to get pass midterms.

The hardest one for you was Biology 101. Thank the Lord you and your friend, Barry Allen, had a little study group. The four of you have been studying for two weeks.

The night before finals was the most… interesting night of studying.

You and Barry were testing the other two, since they claimed that you and Barry were the smartest of the group.

“Ok, Tala, Konrad, you are given this pedigree.” You pointed to a diagram from the book. “What kind of disease is shown?”

The students examined the pedigree. Tala tilted her head. “Autosomal dominant,” she concluded.

Barry smiled. “Correct!” Barry hummed slightly. He spun his pen with his fingers before asking, “What are snRNPs?”

Tala shrugged. “No idea.”

Barry and you looked to Konrad, who was sleeping on the couch. “Konrad!” Barry and you shouted.

The blonde woke up, startled. “The first phase of meiosis! No! The dicot root!” He jolted again when he met the glares of you and Barry. “Sorry, guys. It’s just getting really boring.”

Barry reminded him, “The midterm’s tomorrow. And you don’t know what snRNPs are?”

Konrad shook his head. “It sounds like a badly named Biology term.”

You shrugged. “You’re not wrong. An snRNP stands for small ribonucleoproteins. With the spliceosomes, the snRNPs excise introns during RNA processing.”

Barry smiled. “Impressive, (Y/n).”

“Learned from the best,” you beamed.

Konrad blinked. “I understood nothing.”

“Neither did I,” you admitted. “Flashcards!”

“Still impressive,” Barry commented with a smile. “Come on, guys. Midterm’s tomorrow. Let’s concentrate.”

“I can’t concentrate!” Konrad complained.

Tala suddenly smiled. Her grin turned into a smirk. She whispered in Konrad’s ear something that you couldn’t hear. Konrad grinned. “You know, playing a sort of studying game would help.”

Barry’s face lit up. “I’ll get flashcards.” He pushed himself off the couch.

Tala shook her head. “Not that kind of game.”

Barry sighed and sat back down.You smiled warmly at him, attempting to make him feel better.

Konrad explained, “The game is we keep on going, each person asking a question. Whoever answers the question correctly first has to remove one piece of clothing. If no one answers, then we all do it!” He claps his hands once. “Boom.”

“I came up with that,” Tala scoffed.

Barry immediately went red as cherries. “That’s not a, well, I mean-”

“What he means to say is that if this game goes,” you tried, “um, then, according to you two, Barry and I will be the only ones stripping here!”

“Then, we’ll make the questions easier,” Konrad said.

Konrad and Tala pouted, widening the eyes and quivering the bottom lip.

You sighed. You looked at Barry. “I’m in if you are.”

“Uh,” Barry drawled, scratching the back of his neck. He avoided your gaze.

“Come on, Barry!” Tala insisted. “It’s college! Live a little!”

Barry pursed his lips. “Fine. But only ten questions!”

“Agreed,” Konrad shouted.

The first four rounds were easy enough that Barry and you avoided taking off anything. So far, Konrad has no snapback, and Tala has no sweater, earrings, or a skirt.

However, the fifth question came around. Konrad asked, “What is the nucleotide that goes with adenine?”

Tala completely blanked, (that little liar), and you answered, “Thymine!”

Konrad cheered, “Yea! (Y/n), take something off!” Confidently, you removed your shoes. Then, you asked, “How many pairs of chromosomes do humans have?”

“Four!” Konrad blurted out.

You shook your head.

“46?” Tala guessed.

“No, I said pairs.”

All eyes rested on Barry. The said boy was staring at the empty wall of the dorm.

“Barry, answer it or everyone takes something off,” Tala warned.

He cracked. “23 pairs. We have 23 pairs of chromosomes.” He examined himself. Finally, he decided to take off his shirt.

You bit your lip. You tried to look away, but you just couldn’t will yourself to. Barr Allen didn’t have a six-pack or any abs for that matter, but he was still really attractive without his shirt on.

Barry cleared his throat, red from embarrassment, and you looked away. He opened his textbook and asked, “Ok, now, name one animal Darwin particularly studied in the Galapagos.”

“Lions!” Konrad answered.

“Parakeets?” Tala guessed, (totally knew but faked not knowing it).

You pursed your lips, trying to let someone else answer. “Turtles and finches,” you replied. You removed your earrings.

Tala smirked and asked, “What are the products of photosynthesis?”

Konrad lit up. “I know this one! Oxygen, Carbon dioxide, and glucose!”

Tala shook her head.

You peeked at Barry. He only had pants and underwear left. You sighed and answered before he could. “Oxygen, glucose. That’s it.” You but your lip and removed your sweatshirt, revealing your low-cut tank top.

Barry’s eyes widened, then looked away. Blood rushed to his cheeks. He looked at his lap and fiddled with his thumbs. He cleared his throat.

Konrad was beaming with pride. “Ok, name the four different types of macromolecules.”

Tala responded, “Nucleic acids, lipids, hormones, and proteins.”

“Nucleic acids, lipids, carbohydrates, and proteins,” you answered absentmindedly. You reached for your feet and blushed. You forgot that you already removed your shoes. There were two options, your tank and your bottoms. Blushing profusely, you decided to remove your tank top. You crossed your arms  and looked down. “Barry, your turn.”

When he didn’t answer, you peered at him.

Barry’s mouth was opening and closing, trying to form a coherent sentence. His cheeks were practically tomatoes at this point.

“Barry,” you called again.

Barry coughed and immediately averted his gaze. “Right, um well, what molecule connects the Okawa-”

“Okazaki, Barry,” you corrected.

“What?” Barry turned to you, grew redder, and then looked back to his textbook. “Right. Um. what mole-molecule connects the, um, Okasaks-”


“Yes that. Um, those fragments together?”

“DNA ligase,” Tala answered. She removed her sweater and announced, “The game is over!”

“Aw!” Konrad whined. “Can’t we do a few more?”

“No!” Barry and you exclaimed, grabbing the clothing items that were lost.

You frantically put on your tank top and sweater and packed your things. “Anyway,” you continued, putting on your shoes, “great study sesh, guys. Hope we all do well tomorrow. See you in class. Good night. and all that good stuff.” you were at the door by the time you finished your closing.

Barry was struggling to put on his shirt. You groaned. He was your ride.

Without hesitation, you walked over to him and pulled down the shirt for him. You gasped when you fingers brushed his bare chest. You bit your lip, resisting the urge to show you were affected by the miniscule contact.

Before Barry could even look at you, you left his sight and were at the door again. “Barry, let’s go.”

“Right, uh,” he turned around and then faced you again, “have you seen my backpack?”

You inhaled through your teeth. “Barry, you’re wearing it.”

The young an craned his neck to look at his back. He smiled a little. “Oh, yeah. Ha, um, yeah. Let’s go.”

The ride to the building you two lived in was short but not silent.

You cleared your throat. “Um, Barry?”


“Maybe after the final, we could hang out?” You stared at your lap. “Maybe a date?”

Barry stiffened. His hand slipped and he swerved a little to the side.

“Woah!” Your hand instinctively grabbed his, steadying it. Once the car was on track once again, you let go and cleared your throat. “Sorry, just forget about it.”

“No!” Barry protested. “I mean, I would like to, you know, go on a date. With you.” Satisfied with himself, he nodded. “Yeah. I would like to go on a date with you.”

Maybe it was because you saw each other without a top because of it, but you loved Biology 101 after that.

ANON! WHOEVER REQUESTED THIS IS AN ANGEL SENT FROM HEAVEN!!!! I got really carried away this time guys, but this imagine was super fun to write!!!! I was editing nonstop because i wanted to add so much more to this. 

I actually am in high school, so I hope I managed to capture college decently. I did take Bio AP last year, so I used my AP book for the questions

I know its really long, but I couldn’t bring myself to cut anything else out. So, I hope you guys love it as much I enjoyed the idea, process, and the editing. I actually really liked writing this one. Enjoy! Love you all!!!

the funniest term in biology will always be “srp” or “snRNP”

it’s literally pronounced “snurps”

that just sounds like a meme


Post-Transcriptional Processing

•Only in the Nucleus for Eukaryotes •Primary transcript processed in 3 ways: –1. ADDition of nucleotides –2. DELETion of nucleotides –3. Modification of Nitrogenous Bases •5’ cap and 3’ Poly A tail •snRNP and the Spliceosome of Doom! –INtrons = IN nucleus –EXtrons = EXit the nucleus


Clone Library = plasmid and replication

Polymerase chain reaction (PCR) : ‘fast’ cloning

•Heat to denature •Mix with primers, let cool = primers hybridize •Add polymerase to amplify complementary strands

Southern Blot

•1. Chop up DNA •2. Efield to spread out pieces by SIZE •3. Blot it! •4. Add Radioactive DNA or RNA Probe •5. Visualize on radiographic film  GENETIC CODE •Degenerative – more than one series of nucleotides may code for ANY A.A. •Unambigous = one series of nucleotides = one A.A. •Universal code! •START! AUG •STOP! UAA, UAG, UGA •4^3 = 64 –Ex. protein of 100 A.A. = there are 20^100 possible amino acids sequences for the protein