dna ligase

So I’ve been studying DNA replication at A-Level standard Biology, and since I had so much trouble understanding the concept of it all (particularly the differences between the ‘Leading Strand’ and the ‘Lagging Strand’), I thought I’d upload this here in the hopes that it might aid other people studying the same thing!

In short, nucleotides can only be attached to the DNA strand from the 3′ end, so the strand that has a 3′ end can do this easily and fluidly; this strand is the ‘Leading Strand’. The other strand - the one that has a 5′ end - has to be replicated in stages, and so Primers place free nucleotides further along the strand, from which more can be placed in a 5′ to 3′ direction! each little segment of replicated nucleotides is called an ‘Okazaki Fragment’, and these are finally joined by Ligase!

It can be kind of hard to grasp, so this animation should make it easier. It really is something that is better understood once you’ve seen it visually, after all!! ☆

I hope this is at least helpful, and good luck studying people!

please retain the caption! it gives a better understanding of the post! ♡

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-”

“Okazaki.”

“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?”

“Yeah?”

“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!!!

2

So I was in my room and woke up to the alarm, I dunno what button as usually it beeps but it turned on with NPR’s Morning Edition.   So suddenly, I feel weird, almost like I’m coming up out of ether after being at the dentist or some shit.  It’s almost like it has my attention, and bam, suddenly I’m actually honing in on this nerdy voice talk – seriously you know how Ira Glass sounds, well they all kind of inflect like him.  I guess I start caring and paying attention, which was strange.  I tried to think about it and actually, I always did care about politics and what’s going on in the world, human interest stories, and what’s really perflexing– perplexing, I mean– is, wow,I haven’t been lately.

Perflexing, I think and snort a little snort at my own intentional parapraxis.

I sit up on the bed and pull up my iPhone off the charger.  Swiping through a few screens, check my Facebook, no texts this morning.  I don’t have a shirt on yet and I’m looking at my bare arm and it looks pretty buff, really, and it starts to hit me that something isn’t quite right.  Buff?  I tense up a little and go until the bathroom, running a hand across my face and turning on the sink.  Splashing some water and there’s that big bare arm, definitely got some meat on my shoulders, too.

‘This isn’t right,’ I think, and suddenly it hits me:  I have really been losing myself lately.  I’ve been having fun I guess, exploring some new angles, met this cool new guy who’s been inspiring me but whoa, I am really going down the wrong tracks lately.  I wash up, still hardly believing my own reflection.  Yeah I look healthy, kinda good I admit, but that’s not me.

There’s this pile of hockey gear on the side of my bed and I remember talking about wanting us to work on getting my room more up to speed with this sort of stuff.  I look at my bookshelf, which looks forlorn as if it’s already collecting dust and just not getting any love.  Do I really want to forsake that, push it aside – no, I most definitely don’t.  I sit down on my laptop and log into my Goodreads and click on my profile, just to remind myself what I’ve been reading lately.  Heck, it’s hardly been anything – the last book was weeks ago and not even very challenging – The Price of Salt by Patricia Highsmith?  Sure, I enjoyed Carol, just because it’s Todd Haynes which must be why I got the book, either that or just that they mentioned it on Fresh Air.  But what did I seriously expect out of lightweight lesbian romance from the Eisenhower era – put on a candle and talk about doilies and each other’s hands, it really was mostly a snooze, easy read.

I fire up my iPhone and see what I’ve got in there, but why did I delete so much off my list?  That was stupid of me.  I try to remember what I had in there before, and start adding them back – The Closing of the American Mind by Allan Bloom, Buddenbrooks by Thomas Mann, Dicta and Contradicta by Karl Kraus, maybe Disagreeable Tales by Léon Bloy but nah, it didn’t actually look that good.  Soumission by Michel Houllebecq for sure, as I loved The Possibility of An Island… shit, what else… I feel frustrated.  I should go back to the bookstore and get these added more methodically, as right now it’s just trying to recreate the wheel.  Probably if I spend an afternoon in there, my list will be better than it was the first time, I optimistically tell myself.

I go to make my bed and clean up the place, collecting some empty glasses and putting them in the kitchen, putting that hockey gear in the closet and just as its starting to look nice I get a text.  "Hey man, see ya tonight at 5, you want me to pick up Chipotle or something?“

"Nah I got some food from the farmer’s market here I’ve got to use up, you sure you want to come over?” I text back, hesitant.  This guy!  Even though I appreciate what Chipotle is doing for the organic movement, it’s still corporate and let’s face it, they have really only two items on the menu – a bowl or a wrap, lol.  I really don’t need this guy in my life tonight, I want to get my life back on track and hit up the bookstore.

“Yeah that’s cool, I don’t need to eat, just wanted to swing by and say hi.  Got some books you might love to bring over.”

“Yeah?  I guess, then, I mean just for a little while because I’ve got to study.

I’m big into biology lately, I remember.  Or was always.  Or… shit, I need to hold onto my smart self, who I always was.  I"ll knuckle down on my books, let this bro over for a bit, but that’s the end of it after tonight.  Wow!  Wild ride but this ends tonight, way too much risk of losing myself like I almost did.

I dive deep into my textbook, drilling the vocabulary into my head one word at a time, cognizant of what I’ve lost but it’s coming back quick, thank God.  Submucosa, DNA ligase, disrupter selection, flavin adenine dinucleotide, four fused rings in steroids (a lipid), I’ll get back to the math later, I figure, but at least it’s all rushing back into my mind, no problem there.

Before you know it the doorbell’s ringing, and of course just as I’ve got a candle lit for some nice ambience.  Roasted beets on a bibb lettuce salad with locavore-inspired goat cheese, all organic.  Tamari sunflower seeds and a balsamic vinaigrette, ginger beer on the side, nothing fancy…just a solid meal for a nice night to unwind with.  Nice little wine pairing of a pinot noir, although an aged Riesling would have worked too – beet salad is not a common pairing, I smile, a little smug, I think with a tinge of self-shaming that I tell myself I shouldn’t really have to feel – in how cultured I’ve gotten to be.

I get up and walk over, really not happy that he invited himself over – the guy is a risk, a mindfucker and not good for me.  But I’m firmly in grip of myself and once I get through this night he’ll be easier to blow off for good.

"What are you doing in a t-shirt?” he says just as I open the door, striding past me and sitting right down at the table.

“What was I suppose to wear, a button down for you?"I say back, cockily, knowing I’m the one in control and don’t need to put up with his shit.  Calling his bluff for sure.  I can’t be outwitted by this one, that’s for sure.

"Just seemed odd for you is all,” he says, turning his hat around now that he’s out of the sun and sitting down.

“You’ve eaten already, right?  Because I only made enough for one,” I say, looking him in the eyes.

“i’m still wondering what you’re doing with a t-shirt on,” he says.  "Yeah, I’ve eaten, what do you want to do tonight?“

"I don’t know,” I said after swallowing my bite.  I"m sitting back down and really hate having dinner with him here.  "You’re the one who wanted to come over, remember?“

"Yeah didn’t you want to talk about books or some shit?” he says, leaning back in his chair and kicking off his shoes on my rug.  He should have just taken them off at the door to be polite.

“Sure,” I respond, still looking him right in the eye to make sure he knows who’s in control of the conversation.  "I’m thinking of going to Europe for a few weeks so I’m reading Rick Steves’ Europe 101.  Kind of slight, but fun and actually more informative than you’d think.  Did you know Benedict of Nursia is actually the patron saint of Europe?’

'Oh brother,’ he says, rolling his eyes.  I just keep eating.

He goes on, “Sounds pretty boring to me.  And are you really sure about that t-shirt still, bro?’

He says bro kind of weird, I think, as suddenly at the same time I realize I feel kind of dizzy, like I’m laying back in my chair or.. I think they call it vertigo.

"Don’t call me bro, what the hell are you doing?” I shout across the table at him, annoyed that he’s opening a bottle of wine.  He’s taken off his t-shirt even, big tribal tattoo across his chest, and he knows he looks hot so nobody will question him.  There’s still plenty of pinot in the fridge.

“Calm down, bro, just poppin open a bottle.  God, you’re uptight.’

I am not uptight, I think.  I feel kind of sweaty and constricted by my shirt and realize maybe he has a point, though I’d never admit it.  My pits feel a little damp and it’s like the shirt is annoying or something.  Maybe I just feel warm all over.

"Just sayin that there’s a bottle of wine in the fridge,” I say, trying to eat more just to get this meal over with since I’m not enjoying it anyhow.  I’m hungry and feels good to shovel it in faster even though I know I should savor this more.

'Bro?’ he says, “why don’t you just chill.”

It’s annoying me that he’s calling me bro, or maybe it’s just this shirt that’s annoying me, really.  I wish my arms were free.  "Dude, I’ll be right back,“ I say, just wanted to get out of this at the moment.  I go into my room and open a drawer looking for something.  Don’t see any of my tanks but there’s a singlet, bright red.  That should show him up, I think, plus this t-shirt is just driving me nuts, I think as I strip it off.  Too plain.

I slide the straps over my arms, noticing how cut my torso has gotten.  Something about that kind of excites me for some reason.

I step out, confidentially sitting back down and wolfing down the rest of my food.  Feels a lot better in this singlet, even though it feels weird at first walkin back to dinner barefoot and everything,I know he can see all the hair in my pits and all, even shows some with my guns at my sides, but I kind of like showing him who’s the man here.  Let him play defense.

I slosh down some of this salad – why’d I make some lame salad like this, seriously – with a glass of the wine.  "Here bro, you need a refill?” he says, leanin over and pourin wine in my glass before I even answer.

“I guess,” I say between bites.  "Hey you want to wrestle tonight?“ I say.  Whoa, where’d that come from?  What’s happening?  I don’t even think I feel like myself, all of a sudden.

"Perfect, bro.  He says.  "Who’s your bro?”

“You’re my fucking bro, bro,” I say, thrilled to hear myself just blurting it out.

Before I know it, the tv’s on with the game in the background and this dude has taken off his hoodie and underneath it, he’s in a singlet too, which I like just because I want to practice my wrestling moves.  I’ve been studying so hand and doing all this lame shit and it’s like this guy is an opportunity to connect with the real me, who I just haven’t had time for lately.

I start explaining that to him and he tells me, “hey, listen dumbass, I know the real you.  It’s not that you haven’t had time, it’s that you got lost for a minute.  The real you is a dumb fuckin jock.  You always have been, you are now, you always will be, and we’re gonna hammer that home harder from now on.”

That gets me really excited for some reason and I ask him if he’ll get in referee’s position with me on the top and start off a match.  "Sure, bro, I love to wrestle dumbasses like you" he says.  I love it when he calls me bro.

For no reason at all I start getting a boner, even though I know now isn’t the right time, and though I’m embarrassed, I can’t help myself but say, “I love wrestling man, ok you think I can throw you, you ready to start?”

“We’re gonna have to get a real mat in here soon but yeah I’m ready.  Ok, 3..2..1..” and it’s on.  I’m grabbing at his leg with my left and wrap it around his thick, hairy calf and I try not to think about why I’m amped all of a sudden and how good I’m feelin even as he gets me into a half nelson pretty quick.

Suddenly it’s my skin on his skin, singlet on singlet but for some reason my hardon doesn’t go down.  Then pretty soon he pins me and I’m starin up at him, noticing he hasn’t shaved lately and is getting sweaty and not sure what I’m thinkin because I know I need to focus on the match harder.  Then we’re back in the referee’s position for round two.  He leans over and whispers in my ear, “you look like such a stupid fuckin dumbass primate in that singlet, bro.  I love it.”

“I do?” I say, but it gets me harder for some reason.  Then I blurt out, “You like it when I seem stupid?” I say, knowing how stupid that probably just sounded.

“You are stupid, bro.  But that’s ok because you know all about sports and shit.”

Which is true.  And he’s on top of me and I’m lookin up at him and he flips me, and my hardon brushes up against his thick thigh hard and suddenly my eyes are rolling back in my head and I think I’m cumming… and I cum, all over the front of my singlet, just too much friction or something, don’t know what even happened as this so isn’t like me…“

"Aww bro, what are you doin, dumbass,” he says, suddenly pulling off the straps of his white singlet and sliding it down and I see he has a big hardon himself, which, suddenly I feel like I’m drooling or something and I know what I need to do.

It doesn’t even matter to me that I’ve gotten off cuz this is my bro and I’m so fuckin into it, grateful for how he just got me off, and he pulls me up to my bed and I’m suckin his big dumb dong for what seems like an hour, but I’m lovin every minute of it and wish it would go on forever.  I even start getting hard again and before I know it he throws back his head and moans and hot white sperm is shootin out all over my lips and I lap it up with as much slobber and tongue as I can show just to demonstrate how grateful I am.

This dude, this bro, he’s so cool that he doesn’t even care how fucked up that just was, he lets me crash right out against his muscular biceps on the bed together.

I realize I didn’t set the alarm and then suddenly realize tomorrow is a Saturday and for some reason I don’t want to even deal with resetting it as I’ve had a few glasses of wine and I’m in this moment with my bro so I yank at the cord and it falls out onto the floor into some clothes or something.  My bro laughs his dumb jock laugh and I do too, fucking clocks.  Love weekends.

3

T4 Ligase is an enzyme that is used to bind two strands of DNA together. The Ligase enzyme creates a new bond between the 3’ end of one DNA strand to the 5’ end of another. Ligation reactions are used in molecular biology to insert genes of interest to plasmids for plant / bacterial transformation and cloning.

Thank you so much to everyone that watched my Periscope live stream today! This is the end result of today’s work, an overnight T4 ligation to combine two pieces of DNA for future experiments!

I will be doing more live streams in the future so please be on the lookout for those. If you have Periscope downloaded on your phone, follow me @dailyplantfacts to get notified when I start a new broadcast!

2

Cosima’s notes from Season 1 Episode 8:

“Reverse restriction enzyme through DNA ligase”

“Comp. base pairing”

“DNA ligase”

She is studying recombinant DNA sequences. Restriction enzymes can essentially cut DNA strands into smaller parts, making it easier to analyze and alter. Ligases are another kind of enzyme used to stick these pieces back together or into another organism entirely.

Think Jurassic Park, filling the holes in the incomplete dinosaur genes with DNA from frogs. Or in terms of technology, think of the copy and paste functions of most text editing software. Genetically Modified Organisms (GMOs) are the result, famously used by Monsanto and their patented potatoes.

The clones have probably had their DNA altered slightly from the typical code that 99.9% of all humans share, so it’s pretty safe to say that they would be considered GMOs. An uncomfortable thought, but Cosima seems to be delving fairly deeply into it.

Henderson, M. (2008). 50 Genetics Ideas You Really Need To Know. London: Quercus Publishing Plc.

EDIT: “Group-base pairings changed to Comp. base pairing” because it was late at night and I misread Cosima’s writing. Sorry.