Week 10 Recall Questions

Question 1

A: DNA replication, transcription and gene structure

What does antiparallel mean?

Answer 1

Means the new strand that added to 5’ phosphate —> 3’ with a free OH group [3’ end] —> 3’ stand is being added by 3’ —> 5’.

• 5’ phosphate is attacking the OH group of 3’ end.
• 2 strands Ronn in opposite directions —> allows to predict complementary strand

Question 2

A: DNA replication, transcription and gene structure

What is the mode of DNA replication called?

Answer 2

• Structure of DNA suggests mode of replication —> b/c of precise complementary base pairing —> b/c one of the genetic material requirements was accurate replication of DNA to pass onto next generations

• called semi-conservative replication

• Conservative = parent strand stays intact
• Semi conservative = only one parent strand stays intact, and the other strand is formed by incoming nucleotides

Question 3

A: DNA replication, transcription and gene structure

What is the replication complex?

Answer 3

It is the enzymes that work really close together in the four steps of DNA synthesis.

The entire process as a whole.

Question 4

A: DNA replication, transcription and gene structure

What are the four steps of DNA replication?

Answer 4

Step 1: Strand separation: helicase unwinds DNA helix, starts replication fork

Step 2: Initiation: primase

Step 3: Elongation: DNA polymerase adds DNA nucleotides in 5’- 3’ direction,
No problem for 5’-3’ strand: leading strand = continuous synthesis

Step 4: from DNA replication complex you get two identical, DNA molecules from one parent molecule.

• in eukaryotic organisms, at the end of the chromosome, the DNA strand get a productive cap called telomere, which are nucleotides added by the Telemerase enzymes.

Question 5

A: DNA replication, transcription and gene structure

What is the function of helicase in DNA replication?

Answer 5

(Step 1: DNA strand separation)
- Makes the replication fork

Unwinds the DNA by separating the hydrogen bonds holding the bases of the two DNA strands together.

Leaving 2 parental strands of DNA

Question 6

A: DNA replication, transcription and gene structure

What is the function of primase in DNA replication?

Answer 6

(Step 2: initiation)
- Synthesize RNA primer

Primase enzymes attach a short primer made of RNA (“ RNA primer”) to the DNA templates/parental strands. In order to initiate replication of new DNA stand.

This is necessary, because the enzyme in the next step can only add to existing molecules, therefore, therefore can’t start a new one. And it doesn’t care if it adds to RNA or DNA

Question 7

A: DNA replication, transcription and gene structure

What it the function of DNA polymerase in DNA replication?

Answer 7

(Step 3.1: paring of nucleotide)
- synthesizes an antiparallel strand (5’ —> 3’).
(Step 3.2: paring of nucleotide)
- establishes the phosphodiester bond between sugars of the DNA backbone.

DNA polymerase adds DNA nucleotides to existing DNA molecules/stands (growing strand) while matching it to an existing strand (parental).

It needs the “sticky end” or the reactive OH group at 3’ C to correctly pair the next DNA nucleotide and build the phosphate-oxygen covalent bond we see connecting the nucleotides In the DNA backbone.

• DNA polymerase builds from 5’ C and leaves 3’ C end open.
• follows helicase (move in same direction) —> because it’s one smooth, gliding motion of both helicase and DNA polymerase = called continuous synthesis.

Question 8

A: DNA replication, transcription and gene structure

What is the importance of the 3’OH?

What is the source of energy for DNA repliction?

Answer 8

DNA polymerase specifically needs 3’ C OH group to add onto, which is an existing polymer. = meaning it is what allows nucleotides in the DNA backbone to bind together.

DNA polymerase breaks the bonds between the 1st and 2nd phosphate in the 3 phosphate group connected to 5’ C of one DNA strand —> releases, a lot of energy because this process is hydrolysis —> DNA polymerase uses that energy to bind the remaining phosphate to the OH group connected to a 3’ C of another existing DNA strand —> resulting in elongation of the new DNA strand.

— when you break the bonds between phosphate, the two phosphate released is called pyrophosphate.

Question 9

A: DNA replication, transcription and gene structure

What is the difference in DNA synthesis between the leading and the lagging strand?

Answer 9

Leading strand:
• continuous synthesis
• one DNA strand ≠ no fragments
• uses a single primer

Lagging strand:
• discontinuous synthesis
• produces fragments in 5’ —> 3’ directions.
— not one DNA molecule synthesized but many smaller ones = Okazaki Fragments.

• parental DNA Stand loops around so that the downside of the loop has the same direction as the leading strand.

• loops gets bigger as polymerase builds the strand, once the loop gets too big, the strand that is built is released and a new loop is established.

• each fragment must have a new primer so that polymerase can move along with helicase. (Uses multiple primers)

• Fragments are joined together by enzymes called ligase

Question 10

A: DNA replication, transcription and gene structure

What are Okazaki fragments?

Answer 10

• Because the lagging strand has to loop around in order to move in the same direction as helicase, eventually the loop gets too big and the strand is released.
• and because this DNA strand still needs to be replicated, a new fragment must be started, in order to continue.
• The stopping and starting is what causes breaks in the new DNA strand being built = Okazaki fragments

Question 11

A: DNA replication, transcription and gene structure

What is transcription?

What is the transcription enzyme?

What is the transcription template?

Answer 11

The process of making RNA is called transcription.

The transcription enzyme is RNA polymerase.

The transcription template is DNA.

DNA —> RNA

Information is stored in DNA, which is replicated to allow that information to be passed on.
—>
That information can be copied into RNA, which is either functional in itself or a Messenger to transport that information to the factories where proteins are made.
—>
Ribosomes take that information in the nucleic acid and use it to build proteins for structural and catalytic uses.

• in a non-molecular context, transcription is taking words in one form and copying it down in another form. Such as, transcribing a speech or lecture. Although the form is different, the language is the same.

Question 12

A: DNA replication, transcription and gene structure

How is DNA replication similar to RNA transcription?

How are they different?

Answer 12

Similarities:
- almost have all the same bases and base pairing.
- transcription and replication both depend on the DNA template and base pairing for the sequence of new nucleic acids.

Differences:
- DNA is a long-term memory/information storage.
- RNA can be the messenger/carrier of this information.
- Nature of the daughter strand is RNA instead of DNA.
- DNA has Thymine paired to Adenine
(A-T)
- RNA has Uracil paired to Adenine (A-U)
- RNA polymerase doesn’t need 3’ hydroxyl, like DNA polymerase.
— instead RNA poly can start making a new RNA strand anywhere as long as the sequence is right, and has DNA as a template.
—> promoter on strand is where it binds.
—> transcription start point is where nucleotides start to get added.

Question 13

A: DNA replication, transcription and gene structure

What are different types of RNA?

What is their function?

Answer 13

Transcription produces many types of RNA:

• mRNA: Messenger RNA
- Only these are translated into proteins.
- is not a functional RNA like the rest.
- can’t catalyze rxns on it’s own.

• rRNA: Ribosomal RNA
• tRNA: Transfer RNA

(Not as important to remember)
• snRNA: Small nuclear RNA
• SRP RNA: Signal recognition particle RNA
• siRNA: Small interfering RNA

Question 14

A: DNA replication, transcription and gene structure

What are different products of transcription?

How are they different?

Answer 14

• Transcription unit/coding region: the portion of the DNA that is transcribed into RNA.

• Promoter: defines the transcription start point.
— RNA polymerase binds to it, unwinds double helix of DNA and starts adding RNA nucleotides at transcription start point.
- 5’ to 3’ direction, with 5’ phosphate added onto existing 3’ hydroxyl

• Terminator: a sequence that defines the transcription stop point.
— DNA double helix is rewound and RNA goes away and becomes either a functional RNA, such as tRNA, or is further processed, such as mRNA.

Question 15

A: DNA replication, transcription and gene structure

What is meant by mRNA processing?

Answer 15

Eukaryotes modify their mRNA before translation
• possible because of separation between transcription (in nucleus) and translation (in cytoplasm or ER membrane)

It is when the pre-mRNA in eukaryotic cells undergos 3 processing steps:

Initial piece of RNA that RNA polymerase makes is called primary transcript b/c it still requires chunks (introns) to be removed.

1. Capping of 5’ end.
   - modified G-cap
   = helps protect from exonucleases and with translation.
2. Addition of a poly-A tail on 3’ end
   - bunch of A RNA nucleotides
   = protects from exonucleases and helps direct export from the nucleus
3. Splicing to remove introns.

— helps mRNA from being broken down and signal that it needs to get shipped out of the nucleus to help start translation.

— exonucleases are enzymes that chew up nucleic acid from free ends.

Question 16

A: DNA replication, transcription and gene structure

What is RNA splicing?

Answer 16

The introns are removed from pre-mRNA by the activity of a complex called spliceosome.

• must be able to recognize sequences that are specific to splice junctions (i.e., the end of each exon and the start of the next exon)

Question 17

A: DNA replication, transcription and gene structure

What is the difference between introns and exons?

Answer 17

Exons:
— a segment of RNA molecule containing information coding for a protein or peptide.

Introns:
— are non coding regions that interrupt the gene’s coding sequence.
- are removed and end up with final mRNA.
-not junk DNA

Question 18

A: DNA replication, transcription and gene structure

What are the components or parts of mature (finished) mRNA?

Answer 18

• The modified G-cap on 5’ end.

• Exons.

• The poly-A tail on the 3’ end.

• usually a section of resulting mRNA that doesn’t actually code for proteins, right at the start of the 5’ end and at the end of the strand at the 3’ end. (Before and after coding region)

Question 19

B: Translation and the genetic code

What is needed for translation?

Question 20

B: Translation and the genetic code

What is a ribosome made of?

How many subunits does a ribosome have?

Answer 20

Made of:
- Proteins
- catalytic RNA

It has 2 subunits:
— small subunit
— large subunit

Question 21

B: Translation and the genetic code

What is the function of tRNA?

What are the important sites?

Answer 21

Function:

• aminoacyl tRNA

2 sections of tRNA:

1. Anticodon, which is complementary to the codon in mRNA. A 3 nucleotide sequence that carries the information.
2. Acceptor site, where the appropriate amino acid is covalently attached.

— tRNA can carry one amino acid, however, if there isn’t 1 tRNA for every single codon. This is because there’s something called wobble. Where the third position of the codon can potentially be 1, 2, 3, or all 4 nucleotides.

Question 22

B: Translation and the genetic code

Where are the subunits of a ribosome produced and assembled?

Answer 22

Proteins and RNA are made separately and then assembled in a nucleolus within the nucleus.

The 2 havles of the ribosome are assembled separately, shipped out of the nucleus and then come together and interact with an mRNA to translate a protein.

1. mRNA interacts with small subunit, then big subunit

Quick cheat sheet:
• Subunits assembled in nucleus
• Exist separately in cytoplasm.
• rRNA recognizes mRNA

Question 23

B: Translation and the genetic code

What are the three important sites for translation in a ribosome?

Answer 23

Three sites in ribosome: APE

• aminoacyl, peptidyl, exit

“A, P, E sites”

Question 24

B: Translation and the genetic code

What are the steps in translation?

Answer 24

Initiation:

Elongation:
• Appropriate tRNA goes into A site and rRNA forms covalent bond between the amino acid of that incoming/charged tRNA and the amino acid of the peptide (chain) in the P site.
— which involves breaking the covalent bond between the peptide and the tRNA in the P site (as it’s necessary in order to create new peptide bond between amino acids).

• Now the peptide is bigger by 1 amino acid and the ribosomal proteins bump the newly empty tRNA over into the E site, while at the same time bringing the tRNA from the A site to the P site with its growing peptide chain.
— happens in tandem with mRNA getting shuffled over by 1 codon.

• the empty tRNA in the p slot is given the boot, a new tRNA comes in to interact with the newly presented codon and the cycle continues.

• new codon in mRNA is in A site
• rRNA catalyzes peptide bond formation

Termination:

• a stop codon comes into the A site.

• 3 of them in genetic code and none are recognized by tRNA.

• instead a termination factor comes in. This termination factor is a protein that looks a lot like tRNA and it fits into the A site.

• later on, a release factor breaks the covalent bond between a peptide and the last tRNA in the P site.

• the ribosome dissociates and all the components are released

Question 25

B: Translation and the genetic code

How does initiation in translation proceed?

Answer 25

— initiator tRNA starts in A site (small subunit only)
• carries (recognizes) methionine, AUG in mRNA

— Once the initiator is in place, large subunit binds, bumps tRNA Met into the middle P site.

— Now A site is open and ready for the next tRNA

Question 26

B: Translation and the genetic code

What is a codon and what is an anticodon?

Answer 26

Codon:
— three nucleotide or triplet sequence found mRNA that codes for a certain amino acid during translation.

Anticodon:
— three nucleotide sequence found on tRNA that binds to the corresponding mRNA sequence.

Question 27

B: Translation and the genetic code

What is a polyribosome?

Answer 27

Is a group of ribosomes bound to an mRNA likes “beads”, which simultaneously translate, the same mRNA.

• The further down you travel the DNA strand the longer the polypeptides will be.

• consists of a complex of an mRNA molecule and 2 or more ribosomes that act to translate mRNA instructions to polypeptides.

Question 28

B: Translation and the genetic code

How is translation initiated in prokaryotes?

Answer 28

There’s no modification of mRNA, this is because the mRNA is available to the translational machinery, even as it’s being transcribed.

Therefore, you will observe a polyribosome. Which is a DNA strand that has many ribosomes attached to it translating. If you look closer at the ribosomes would be able to see polypeptides coming out of them, getting longer as you go further down the DNA strand.

Another reason why translation can start before transcription is finished, is that the ribosomes recognize a specific sequence in mRNA; the ribosome binding site, which corresponds to a specific sequence in one of the rRNAs (ribosomal RNA).

Nucleotide interaction is important. This doesn’t occur in eukaryotes because that part of translation is more complicated and the mRNA has to be circularized before translation can even begin.

In some bacteria the ribosome recognizes the ribosome binding site, and then start translating at the first AUG after that.

Question 29

B: Translation and the genetic code

How and where is translation initiated in eukaryotes?

Answer 29

The finished and modified mRNA is exported from the nucleus in the cytoplasm, from there two things can occur.

1. The resulting water soluble proteins is needed in the cytoplasm so ribosomes attached and translation begins.
2. The protein will be water, insoluble and function within the membrane, or that the protein will be exported from the cell.

In either of these cases, once a ribosome recognizes the mRNA, it brings it over to the rough ER and docks it in the membrane. Then the peptide is translated either into the lumen or directly into the membrane.

Once translation is done, the ribosome dissociates, and the 2 halves float off to find another mRNA.

Question 30

B: Translation and the genetic code

What are the differences in translation between prokaryotes and eukaryotes?

Answer 30

Pro:
- polyribosomes
- can start translation before finishing transcription.
— mRNA needs to be circularized
- no modification of mRNA

Eu:
- no polyribosomes
- can only start translation after transcription is finished.
- modification of mRNA

Question 31

B: Translation and the genetic code

Where are proteins synthesized that function in the cytoplasm?

Question 32

B: Translation and the genetic code

Where are proteins synthesized that become part of the plasma membrane or that will be exported?

Question 33

B: Translation and the genetic code

What is a reading frame and why is it necessary?

Answer 33

The reading frame is the way the ribosome group the nucleotides of the mRNA into a sets of three.

It is critical that the ribosome has the right reading frame, or what comes out is absolute nonsense.

Once the reading frame is determined, the ribosome reads that frame for the rest of the transcript.

Therefore, it’s important to start at the correct start codon.

Question 34

B: Translation and the genetic code

What determines the reading frame?

Answer 34

The ribosome always starts with a AUG. But how the ribosome determines which AUG depends on if we’re talking about prokaryotes or eukaryotes

Question 35

B: Translation and the genetic code

What is a codon table?

Answer 35

A table that you can use to figure out which amino acids are coded for by a given sequence, and which sequence could be used to code for a particular sequence of amino acids.

1. Look at the left side of the table for the first base of the codon.
2. Read across the table for the second base.
3. Look at the third base is within the box.

( which codon(s) direct the addition of which amino acid.)

Question 36

B: Translation and the genetic code

What is the start codon?

Answer 36

The start codon is AUG

Question 37

B: Translation and the genetic code

What are the three stop codons?

Answer 37

1. UAA
2. UAG
3. UGA

Question 38

B: Translation and the genetic code

What happens at the termination of translation?

Answer 38

A stop codon in the mRNA enters the A site.

• A termination factor, which is a protein that looks a lot like tRNA fits into the A site, then this factor/ or stop codons are recognized by proteins called release factors, these fit into the P site.

• release factors messes with the enzyme that normally forms peptide bonds with.
— causing it to add a water molecule to the last amino acid of the chain.

• This reaction separates the chain from tRNA and the newly protein is released.

• the ribosome dissociates and all the components are released.