Cell and Molecular Biology: Transcription + Translation- Chapter 11.1

Chapter 11.1

Review the flow of information through a cell and be prepared to discuss it including the types of RNA involved (do not write it down).

1. DNA transcribed to RNA (in the nucleus), translated to protein (DNA→DNA is replication) (outside the nucleus);
2. types of RNA include t, m (messenger, DNA→RNA), and rRNA;
3. RNA isn’t just a straight line, it has folds and crusts and even some base pairing with itself.

Discuss the basic process of transcription.

1. First, base pairing between DNA and RNA in an enzyme called RNA polymerase
2. This causes an RNA strand to form
3. With the promoter being the place where the polymerase binds
4. Transcription factors (which are proteins) help the polymerase bind to the promoters so transcription can occur

Review the flow of information through a cell and be prepared to discuss it including the types of RNA involved (do not write it down).

1. DNA transcribed to RNA (in the nucleus), translated to protein (DNA→DNA is replication) (outside the nucleus);
2. types of RNA include t, m (messenger, DNA→RNA), and rRNA;
3. RNA isn’t just a straight line, it has folds and crusts and even some base pairing with itself.

Discuss the basic process of transcription.

1. First, base pairing between DNA and RNA in an enzyme called RNA polymerase
2. This causes an RNA strand to form
3. With the promoter being the place where the polymerase binds
4. Transcription factors (which are proteins) help the polymerase bind to the promoters so transcription can occur

Discuss the basic process of transcription.  Be sure to include the enzyme required, the function of the promoter and transcription factors, the directionality of the process and the importance of pyrophosphate.

1. Directionality

   1. The RNA is synthesized 5’ to 3’ since polymerase can only add to the 3’ end (and the DNA is being read 3’ to 5’)

2. NTPs (ATP, GTP, and more) are the precursors that are used to create DNA and RNAD, along with Mg+2, they have 2 of their phosphates removed in order to make pyrophosphate (which is broken up into individual phosphates)

   1. If you cut off diphosphate, then 2 phosphates replace it

3. Importance of pyrophosphate

   1. This causes a very large energy release making the RNA formation reaction irreversible. Transcription happens at multiple spots along the DNA

Prokaryotic transcription: core enzyme

Single type of RNA polymerase made of 5 tightly associated subunits

Prokaryotic transcription: sigma-factor (protein)

Protein that causes the core enzyme to start transcription at selection locations (promoters), in position to randomly (with the sigma-factor coming off after transcription starts)

Prokaryotic transcription: holoenzyme

Complete enzyme made when the core enzyme and sigma factor bind

Prokaryotic transcription:

1. Sequence common among all promoters (quite similar; however, not exactly the same sequence).
2. This is important in getting the polymerase to bind (as it recognizes these things)

What are the two consensus sequences in the prokaryotic promoter?

1. TTGACA at about -35 (bases upstream)
2. TATAAT at about -10

NOTE: the sequences are always going to be named 5’ to 3’

Name and describe the function of the five eukaryotic RNA polymerases.

1. Each of the 5 Eukaryotic RNA polymerases synthesizes a different kind of RNA

   1. I: synthesizing larger rRNAs (28S, 18S, 5.8S)
   2. II: synthesizing mRNAs, most small nuclear RNAs (sn and snoRNAs), most microRNAs, and telmoerase RNAs
   3. III: synthesizing other small RNAs (t, 5S r, and U6 and snRNAs)
   4. IV + V: only found in plants; synthesizing siRNAs

2. Eukaryotic polymerases have the cores of the prokaryotic polymerases (they are homogenous)

Eukaryotic RNA polymerase 1

synthesizing larger rRNAs (28S, 18S, 5.8S)

Eukaryotic RNA polymerase 2

 synthesizing mRNAs, most small nuclear RNAs (sn and snoRNAs), most microRNAs, and telomerase RNAs

Eukaryotic RNA polymerase 3

synthesizing other small RNAs (t, 5S r, and U6 and snRNAs)

Eukaryotic RNA polymerase 4+5

only found in plants; synthesizing siRNAs

Discuss the concept of a primary transcript and RNA processing.

If you are going from DNA to RNA, there is a primary transcript which is modified later into the final product/form by processing it into something shorter (such as cutting off and stitching together)

Describe the structure of a mammalian ribosome including subunits, proteins and types of RNA.

1. Made up of 2 subunits

   1. A large (60S) and small (40S) subunit (the whole thing is 80S)

      1. Large: made up of 49 ribosomal proteins and a 28S, 5.8S, and 5S rRNA
      2. Small: 33 ribosomal proteins and an 18S rRNA

2. S is based on centrifugation, with larger things moving down farther than the smaller things; therefore, it is related to the distance down it went

   1. However, not additively, b/c related to both shape and mass

3. The prokaryotic ribosomes are different from eukaryotic (mammalian) ribosomes

4. ^^RNA makes up the bulk of the ribosome’s structure; not the protein^^

Define rDNA

DNA that encodes rRNA

How much rDNA is present and how is it organized in the genome?

1. These sequences are repeated up to hundreds of times, they are clustered together as nucleoli that make ribosomes (or during cell division, are clustered on 5 different chromosome clusters)
2. The $45S gene is moderately repeated (600 total repeats that are found in 5 diff. Chromosome clusters$) in order to make sure we can make a lot of them easily, and it is used to make the nucleolus

Nucleolus structure

• The bulk is a granular compartment with ribosomal subunits in different stages of assembly,
• it's embedded with fibrillar centers (fc) surrounded by a more dense fibrillar component (dfc),
• with the fc containing DNA that codes for 45S rDNA,
• the dfc containing rRNA transcripts (coming from the rDNA) and associated proteins,

Functions of the different regions of the nucleolus

1. The $overall function is to make ribosomes$, this is $located in the$ $nucleus$ (its the proteins needed for those that start outside the nucleus and come inside)

2. and $transcription of the pre-rRNA precursor$ takes place at the border between the fc and dfc.

   1. There is a very large number of these in eggs that have not yet been fertilized

What rRNAs are derived from the 45S rRNA primary transcript?

32S, 18 S, and 5.8S RNA

What are snoRNPs?

• $snoRNPs are small, nucleolar ribonucleoproteins$
  • that $store small pieces of RNA$ (snoRNA, small nucleolar RNAs) and some protein, and it helps to do particular tasks as part of $rRNA processing$

snoRNP’s function

1. By base pairing with the in-process RNA

   1. Ex: by modifying the bases (like methylation) after transcription

2. They associate with the rRNA precursor before it’s fully transcribed, removing the 5’ end of the transcript.

3. It is modified through unimportant pieces being cut off, while the 3 sections that are kept being 18S, 28S, and 5.8S

What does the RNA do in these structures?

1. 45S is the primary transcript, then an enzyme comes in and cuts away pieces to leave behind the 3 pieces as the 3 final transcripts that are detached from each other
2. This is causing the $rNAS$ that are part of the larger mammalian ribosome, with these 3 RNAs coming from the 45 S gene

How many 5S rRNA genes are there and where are they located?

It is encoded by a large number of identical genes (moderately repeated, $35-175$) on chromosome 1, and is separate from the other rRNA genes by being located on the $outside of the nucleolus$ (the initial transcript is bigger than the 5S gene, and the extra stuff is cut away, down to 120 base pairs

How many tRNA genes are there in a typical cell?

There are about $40-60 different tRNAs made up of 1300 genes$ (moderately repeated) in a typical cell, although there are some that are repeated at different amounts in different organisms