chapter 17:

Question 1

t/f during transcription RNA polymerase uses a DNA template to make a complementary RNA.

Answer 1

t

Question 2

What is RNA polymerase?

Answer 2

uses DNA as a template, and make a new complementary nucleic acid based on the sequences of that template, and will then produce anther molecule of RNA.
- binds then moves three prime to five prime along the template strand as it synthesis the new RNA 5 prime to 3 prime.

Question 3

The strand of DNA that is transcribed by the RNA is known as what?

Answer 3

template strand

Question 4

T/F you can tell which is the template strand just by looking at it?

Answer 4

False.

Question 5

t/f the RNA strand should be the same as the none template strand, aside from the u vs t thing?

Answer 5

true, if all goes as planned.

Question 6

How does RNA polymerase know where the beginning of the gene is so it may bind at the beginning?

Answer 6

• at the start of each gene there is sequence of genes that act as promoter.

Question 7

What is a promoter?

Answer 7

• the promoter is not transcribed itself, but it is the side where RNA polymerase is recruited the gene and then the regions after that get transcribed.

Question 8

What does a +1 mean?

Answer 8

it is the first base that gets transcribed

Question 9

What is a sigma?

Answer 9

In prokaryotes: a protein that binds to the promoter region of the gene and then RNA polymerase binds to Sigma, thus assembling RNA polymerase to the promoter at the correct site.

Question 10

What is a holoenzyme?

Answer 10

the combination of an RNA polymerase and a sigma.

Question 11

How transcription initiated in bacteria?

Answer 11

• the holoenzyme binds to the promoter.
• there is four channels connected to a central chamber .
• The DNA strand is passed through the central chamber, where it is split by the two nobs in the middle.
• the enzymatic activity is concentrated to a lower region in the thing, this is where the new phosphodiester bonds are made.
• the ribonucleotide triphosphates flow in through the bottom region of the chamber and then complementary base pairs to the template strand.
• the rutter, which is the second nob in the image pushes the new strand out the other hole in the chamber.
• this continues until the RNA runs into a termination signal.
  ( look at example in notes while doing)

Question 12

What is the termination signal in bacteria?

Answer 12

sequence of bases that will encode a messenger RNA that has some internal self complementary.

• meaning they can fold up and make some internal hairpins.
• the hairpin folding helps aid in pulling the RNA strand out of the chamber and once that is done the termination signal is commenced.

Question 13

How is transcription in eukaryotes different?

Answer 13

eukaryotes have three different versions of RNA polymerase

• they don’t use sigma.
• if your talking about a protein coding gene the initial RNA that is made from RNA polymerase 2 of that gene is not a functional RNA. it has to be processed in a certain kind of way in order to become a functional rna

Question 14

What types of genes do RNA polymerase 1 encode for?

Answer 14

• genes that code for most of the large RNA molecules (rRNAs) found in ribosomes

Question 15

What types of genes do RNA polymerase 2 encode for?

Answer 15

• protein coding genes that will encode a mRNA

Question 16

What types of genes do RNA polymerase 3 encode for?

Answer 16

Genes that encode for tRNAs and small rRNA’s

Question 17

What is splicing?

• why it occurs?
• the steps behind it
• important molecules for the overall process?

Answer 17

• Helps process primary RNA to mRNA
  in eukaryotes, genes that encode proteins have the protein coding information broken into chunks, referred as exons.
• and exons are separated by introns that don’t actually contain any genetic information for the protein.
• so the initial RNA has both introns and exons, it is also known as the primary RNA transcript.
  -the spliced RNA is just the exons stitched together.
  ——————————————————————————
  mediated by a class of molecules called snRNPs.
  —————————————————————————–
  the snRNPs assemble on exon and intron borders, loop out the intron and cut it on both ends and then stitch together the ends of the exon.
• the intron loop portion is simply degraded or cut out.

Question 18

What post-modifications occur in eukaryotes?

Answer 18

• Helps turn primary RNA to mRNA
  the ends of RNA must be modified.
  —————————————————————————
• there is a five prime cap that contains a methylated guanine.
• ## at the three prime end there is an enzyme that recognizes a sequence at the three prime end of the messenger RNA and then adds a long chain of adenines (poly A tail) .these modifications are important because they:
  protect the coding region of the mRNA
• the help to interact with proteins that will get the mRNA out of the nucleus and into the cytoplasm
• they can interact with proteins that will anchor the mRNA to a particular region of the cell.

Question 19

t/f In bacteria transcription and translation occur independently?

Answer 19

false, the can happen simultaneously because the DNA and the ribosomes are all encapsulated in the nucleus

Question 20

describe the process of ribosome transcription/translation in prokaryotes?

Answer 20

• RNA polymerase binds to the gene and starts to transcribe the gene, as it is making the mRNA a ribosome can bind.
• then the ribosome can start translating the mRNA so protein synthesis can start occurring shortly after
• you can also have multiple ribosomes translating the same mRNA (polyribosome)

Question 21

Describe the process of transcription/translation in eukaryotes?

Answer 21

• transcription and translation occur in differing parts of the cell.
• the initial transcript that is produced in transcription has to be spliced and turned into a functional mRNA
• mRNA is then transported to the cytosol
• ## mRNA is then translated at the ribosome.therefor these process occur at differing times and places.

Question 22

how do codons and amino acids interact?

Answer 22

Adapter molecules hold amino acids and interact with mRNA codons.

• tRNA served as the adapter molecules
• tRNA fold up to make a triple hairpin structure.
• one end contains an anti codon
• on the other end at the three prime end there is an amino acid attached. this is known as an aminoacyl tRNA.
• There is an aminoacyl for every codon.

Question 23

What is an anticodon?

Answer 23

• seen on a tRNA, it is a reverse complement of a codon.

Question 24

what is aminoacyl tRNA synthetase?

Answer 24

• this is an enzyme that binds to tRNAs, and recognizes what anticodon is here and then attaches the appropriate amino acid.
• there are different types of synthetase for the varying types of aminoacyl tRNAs.

Question 25

What are the subunits of ribosomes?

Answer 25

• large and small

Question 26

Describe the ribosome in the middle of translation?

Answer 26

• there are three chambers A, P, E
• the A site holds the next aminoacyl tRNA.
• The P site holds the previous one
• The E site holds the tRNA that has lost its amino acid
• The ribosome will be moving down the mRNA, and every time it moves there is a new codon under the A site, thus allowing a new aminoacyl tRNA to come in.
• the top chamber is where the peptide chain is being assembled and projects out the top of the ribosome.

Question 27

How is translation initiated in bacteria?

Answer 27

• There has to be something to help position the ribosome near the start codon (AUG)
• the positioning is a result of a specific sequence of bases in the mRNA, just upstream, just 5 prime to the start codon, that is complementary to the sequence of bases in one of the ribosomal components of the small sub unit
• green globs located in between the large and small sub unit of the ribosome is known as initiation factors, which serve to assist in actions between the mRNA and the ribosomal subunit.
• essentially when the mRNA binds on to the small subunit the initiation factor is right near the small subunit , which helps stabilize the Aminoacyl tRNA carrying methionine.
• Following this the large subunit sits down so that this first amino acid is in the p site, leaving us with vacant A and E sites.

Question 28

What is elongation and what happens in it?

prokaryote

Answer 28

• describes the Ribosome moving down the mRNA from the 5 prime to the 3 prime and incorporating the right amino acids as it moves.
• aminoacyl tRNAs flow into the A site, and if it contains the anticodon that is complementary to the next codon then it is going to stick, thus positing the amino acids above of the previous and the current next to each other. this location catalyzes the formation of phosphodiester bonds between amino acids.
• following the formation of phosphodiester bonds the aminoacyl tRNA in the cambers become just tRNA’s as their amino group has been striped.
• then A goes to P, P goes to E, and E goes to exit.

Question 29

When does elongation end?

prokaryote

Answer 29

• When the RNA has reached the stop codon.
• this is because there aren’t any aminoacyl tRNA that recognize the stop codon, so there are protein’s called release factors that are shaped like tRNAs and recognize the stop codon.
• the release factor slides in, because there is no more aminoacyl tRNAs, and it takes up the site.
• now that there is no more amino acids that could be added so the poly peptide chain falls out and it can begin to fold in the cytoplasm.
• then the large subunit falls off and the small subunit falls off. The mRNA is separated and the mRNA can be translated again, as can the large and small subunits of the ribosome

Question 30

What are polycistronic genes?

- what organisms are the most prevalent in?

Answer 30

• prokaryotes.
  genes that make a mRNA that has multiple ribosome binding sites, start sites and stop sites.
• which allows it to encode for more than one protein .

Question 31

What is alternative splicing, and what organisms use it?

Answer 31

• Eukaryotes use that bitch.
• sometime when introns are being removed one or more exons also get removed.
• so when the same gene is spliced differently each time there is chance to get a slightly different protein each time as well.
• occurs in different cells.