Transcription

How many mRNA copies can you make from the DNA?

You can make as many mRNA copies from DNA as long as you leave the original in the nucleus.

How fast can you transcribe DNA? How many bases per second?

You can transcribe DNA 50 bases per second.

How do nucleotides relate to genes?

A chromosome is a strand of DNA that carries genes and are generally found in the nucleus of cells. Nucleotides are the building blocks of DNA and RNA. They are composed of a nitrogenous base (cytosine, adenine, guanine, thymine, or uracil), 5-carbon sugar (ribose or deoxyribose), and one or more phosphate group(s).

How many genes (about) do we have?

About 21,000 genes are essential to human function.

Which 4 nucleotides make up RNA?

Adenine, Guanine, Cytosine or Uracil.

What happens to the spliced (finished product) mRNA?

After splicing, introns are removed and exons are joined together (ligated). For nuclear-encoded genes, splicing takes place within the nucleus either co-transcriptionally or immediately after transcription.

Does just the gene get transcribed into RNA, or all the junk around the gene?

All the junk around the gene gets transcribed! Both exons and introns.

What is the Central Dogma?

Central Dogma describes the two processes transcription or transcribe and then translation. Online Definition: The central dogma of molecular biology describes the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → Protein → You. This 4 step process is called the "Central Dogma".

Whose rules do you follow to figure out how to make an mRNA copy from DNA?

Chargaff's rules!

Does DNA ever leave the nucleus?

DNA NEVER leaves the nucleus! It only transfer information out of the nucleus into translation also known as the proteins!

How does mRNA it leave the nucleus?

DNA transcribes mRNA for the appropriate gene, and the mRNA is then exported out of the nucleus through pores in the nuclear membrane into the cytoplasm. Here, the mRNA builds the proteins that perform cell functions or serve as building blocks of larger proteins.

How do RNA and DNA differ? Can you think of 5 ways that they differ?

DNA: "The original" 2-stranded Must stay in the nucleus Deoxyribose sugar "Nucleotide" language (similar to RNA) C,G,A,T RNA: "The copy" 1-stranded Leaves the nucleus Ribose sugar "Nucleotide" language (similar to DNA) C,G,A,U

What are the 3 steps of transcription? What happens in each?

First Step: RNA polymerase unzips the DNA double helix (Initiation) Second Step: Get the RNA in the DNA and see/read/get what you need and start copying. RNA polymerase builds mRNA on the new template Strand by adding bases' on the 5' to 3' direction. (Elongation). Third Step: The mRNA that is formed leaves the nucleus. (Termination).

Can you think of an example of a gene (protein) that fits each of the 3 patterns?

Housekeeping - maintain pH balance Survival - produce protein to clog a cut Ontogeny - turns on then off forever the genes that you use in the beginning, breathing using the umbilical cord

What are 3 "patterns" of gene expression?

Housekeeping genes #4 Survival genes #6 Ontogeny - i.e, fetal development or puberty

How do they differ?

Housekeeping genes - Are always working 24/7/52/107! They remain keeping your insides healthy. It's what maintains the water balance of all cells, and protein that maintain the pH balance of all cells. They also regulate salt content! Survival genes - Everybody's out to grow, survive, and reproduce. (Specifically, here, I'd like you to think in terms of OFF until turned ON. Doesn't necessarily need to just be survival, but anything like a light switch where you keep it turned off until you need it and then you turn it on) Ontogeny - On and then forever off.

What will happen if you don't transcribe enough?

If you transcribe too little protein it'll lead to inadequate function and fall apart.

What will happen if you transcribe to much?

If you transcribe too much protein we'll be wasteful and energetically dangerous!

How do they relate to the physical challenges of DNA replication?

In DNA replication, one of the very first steps we had to do was also unwind the double helix and split it into two strands by breaking the hydrogen bonds.

Why is it important to carefully control transcription?

It's important to control transcription because if we don't it'll fall apart and lead to inadequate function.

Why is it OK for it to be single stranded?

It's ok to access only one single strand because if you know one strand you'll know the other strand because Chargaff's rule dictates what the other one has to be.

What does the "m" stand for in mRNA?

M = Messenger

When DNA is ready to be read (transcribed), it must obviously unwind. Does the DNA need to be cut?

No the DNA does not need to be cut. It is unwind just enough to get that RNA and see/read what you want. You need to break the ionic bonds that hold the two strands together, but you don't need to cut the actual DNA molecules

One way that they are the same?

Nucleotide language!

So how many strands of the DNA do you need to access?

Only one strand according to Chargaff's rule.

Where do these 4 nucleotides come from?

Original DNA

What do we call the section of DNA that acts as the starter region to attract RNA polymerase?

Promoter

How important is protein synthesis?

Protein synthesis can also be seen as transcription which is the process by which information in DNA is copied into a new format. Because DNA is in the nucleus and ribosomes are in the cytoplasm, your cells need to rely on RNA, or ribonucleic acid, to transfer the information so protein synthesis is important!

What is the name of the enzyme that synthesizes mRNA?

RNA POLYMERASE = SYNTHESIZES mRNA from DNA

When the information in DNA is transcribed to RNA, is the RNA molecule made single or double stranded?

RNA molecule is made single stranded.

What does a gene usually "make" (or "code for")?

Segments of DNA called "genes" are the ingredients. Each gene adds a specific protein to the recipe. Genes makes our physical traits!

The substitution of uracil for thymine?

Since you're transcribing DNA into RNA Thymine must substitute into for Uracil. So, to be clear, DNA uses G,C,A, and T, and RNA uses G,C,A, and U

Does mRNA splicing happen inside or outside the nucleus?

Splicing happens inside the nucleus.

Can you describe the flow of information from DNA to protein?

Step 1 (DNA): DNA is going to have sections called a "gene" and it's going to code for a specific protein. Then we will copy that gene into the messenger RNA... (mRNA) and this process will be called Transcription. Step 2 (RNA): Both step 1 and 2 will take place in the nucleus. We're going to manipulate that RNA and then move out through one of these nuclear pores. You're getting the information out of the nucleus. Step 3 (Protein): Both step 3 and 4 will take place in the cytoplasm now and this process is called Translation. Once the mRNA has moved out into the nuclear pores, it's going to grab onto the ribosomes and it's going to make proteins. These amino acids are going to weave together and eventually create a protein. Step 4 (You): In the very last step, the protein makes US! (We're made up of a bunch of different proteins).

What are 3 ways to carefully control the rate of transcription?

Step 1: Limit access to DNA Step 2: Control the activation of your mRNA via splicing. (You can make the RNA and leave it in an inactive form and later on splice it and make adjustments to get it ready and this will help you control the flow through here) Step 3: Control export of mRNA through the nuclear pore and out into the cytoplasm. (You can control the passage just like the gate and control who goes in and out and you can adjust the rate at which the mRNA isn't allowed to go out of the cytoplasm).

What do we call the section of DNA that tells the RNA polymerase to jump off the DNA and stop transcription?

Termination

Can the mRNA ever leave the nucleus?

The DNA stays in the nucleus, but the mRNA leaves through the nuclear pores to go out to the cytoplasm to get to the ribosomes for translation.

If the junk gets transcribed, what happens to the RNA transcription of the junk?

The intronic parts are light pink and are useless and don't code for anything. You can just leave inactive or you can splice it and put pieces together.

How is RNA different from DNA? Is it the sugar?

The sugar found in DNA contains one less oxygen molecule than the sugar found in RNA.

What are some physical challenges with transcription?

There are 2 physical challenges with transcription! - Need to unwind the double helix - Need to split the two strands DNA Polymerase's job is to do these two physical jobs for transcription!

How does RNA polymerase know where to jump onto the DNA and start transcription?

There's a green strand called the "promoter" and this strand tells the RNA where to stick on and where to bind. It's going to be in a downstream direction (left to right).

What is transcription?

Transcription is the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA). DNA safely and stably stores genetic material in the nuclei of cells as a reference, or template. Transcription takes place in the nucleus!

How does transcription relate to the central dogma?

Transcription is what makes the central dogma. Central dogma = the two step process of both transcription and translation.

Why does it leave the nucleus? Where is it headed? Why?

Transcription takes place in the nucleus. It uses DNA as a template to make an RNA molecule. RNA then leaves the nucleus and goes to a ribosome in the cytoplasm, where translation occurs. Translation reads the genetic code in mRNA and makes a protein.

The DNA is copied into mRNA?

Yes DNA is copied into mRNA.

Can you transcribe a DNA strand into RNA? Remembering to switch in uracil for thymine?

Yes and yes!

DNA holds the proper information to direct all of life. Transcription is the process by which DNA information is transferred to RNA.

Yes it is!

Is exit of mRNA from the nucleus controlled?

Yes you can control of which the mRNA goes out into the cytoplasm via nuclear pores as ribosome machinery translate the mRNA into protein.

Can you picture how the physical arrangement of DNA (chromatin vs. chromosomes) helps to control access to the genes, and therefore the rate of transcription?

Yes!

Can you see the whole picture of where genes live on chromosomes, and how genes are made up of long stretches of DNA?

Yes! Specifically, in chromatin form, it can be accessed, in chromosome form, the DNA is too dense and packed together to access any individual strand of DNA to transcribe it

How does this splicing control the rate of transcription?

You keep it in an inactive form then later you will activate it again. The rate at which you activate it by splicing controls the rate of which mRNA goes out into the cytoplasm. Therefore, it controls the rate at which you turn this gene into protein.

How many nucleotides are usually in a gene?

You've got six billion of these pairs of nucleotides in each of your cells, and amongst these six billion nucleotide pairs are roughly 23,000 genes. A gene is a distinct stretch of DNA that determines something about who you are.