D1.2

Question 1

Transcription

Gene Expression?

Synonomous with Protein Synthesis

Answer 1

• The using of the instructoins in a gene (segment of DNA that codes for one protien)

Question 2

Transcription

What is transcription?

Answer 2

• This is the first step in protein synthesis
• Involves building/making/synthesizing a strand of messenger RNA(mRNA) from the template DNA for a single gene
• DNA can’t leave the nucleus to get to the ribosome, so a copy that can is made.
• The mRNA is only a copy of the single gene being used at that time - is signle stranded in order to leave nucleus via a pore.

Question 3

Transcription

What is the template strand?

Answer 3

• As mRNA is single stranged, only one of the two strands of DNA need to be copied.
• The one that is copied across is the template strand (provides info on what RNA bases to add)
• Other strand isn’t directly used is transcription but its sequence will match new mRNA (except will have T instead of U - called the sense/coding strand)

Question 4

Transcription

What is messenger RNA?

mRNA, one of a few different types of DNA.

Answer 4

• The single strands that are copies of the template DNA
• They carry the instructions/ MESSAGE from the nucleous to the ribosomes
• Copies URACIL instead of thymine.

Question 5

Transcription

What is the transcriptome?

Answer 5

• The actual DNA bases that will be transcribed into mRNA to make proteins - they copy the exons on the template strand (genome)
• Some of the DNA bases in the genome don’t code for proteins, thus the transcriptome is only the ones that do.

Question 6

Transcription

What is a promoter?

Answer 6

• A section of DNA that is ahead of the gene and shows RNA polymerase where to bind in order to begin transcription.
• Common promoter is called TATA box (series of Ts and As at the end of the promoer) as they are easy to break (only 2 H-bonds) to divide DNA to start transcription.

Question 7

Transcription

What are transcription factors?

Answer 7

• Proteins that bind to the promoter to either promote & start transcirption or bind and prevent it.
• Lots of promoters have both activator and repressor sequences so different types of transcription factors can bind.
• Most genes need transcription factors for DNA polymerase to bind for transcription to begin

Question 8

Transcription

What are the 4 main functions of DNA polymerase?

Transcription dependent on DNA polymerase

Answer 8

• Unwind the helix into two strand
• Move along the template strand positioning complementary RNA nucleotides
• Create phosphodiester bonds between RNA nucleotides
• Detach RNA from the DNA so it can reform into a helix.

Question 9

Transcription

Explain the directionality of transcription

Answer 9

• As mRNA is single stranded only one side copied
• RNA polyermase adds nucleotides to a 3’ end of a nucleotide - 5’–>3’ strand
• Thus, transcription only makes a leading strand

Question 10

Transcription

Compare sense vs antisense strands.

Note the template strand is also called the antisense/non-coding strand

Answer 10

• Antisense(non-coding): the strand that RNA polyermase uses to build complementary RNA.
• Sense (coding): Has the same bases as the mRNA (except has uracil) but it not the strand used by RNA polymerase

Question 11

Transcription

What are the complementary base pairs in transcription?

Answer 11

• In Transcription, a DNA base of Guanine results in an RNA base of Cytosine
• Likewise, a DNA base of Cytosine will result in an RNA base of Gaunine being added
• A DNA base of Thymine results in an Adenine base being added.
• HOWEVER a DNA base of Adenine results in an RNA base of URACIL being added.

Question 12

Transcription

Compare the transcriptome vs the Genome

Answer 12

• GENOME: every SINGLE base of DNA, including those that don’t code for proteins (telomers, promoters, introns).
• TRANSCRIPTOME: all the mRNA bases that will be made (or all coding DNA bases) - much smaller than genome.

Question 13

Post-transcriptional Modification

What are exons?

EXit the nucleus. They are EXtremely important.

Answer 13

• Coding sections of DNA within a gene that will be maintinaed the the mature mRNA and directly used as codons that code for amino acids in the making of proteins.
• They therefore leave the nucleus and go to the ribosomes

Question 14

What are introns?

Prokaryotes do not have them

Answer 14

• Sections of the DNA that are within the coding region of the gene but which do not carry sequences used for amino acids
• Non-coding DNA WITHIN the gene
• As they’re not instructions for amino acids, they are spliced out in the nucleus before it leaves.

Question 15

What are spliceosomes?

Name and function

Answer 15

• An RNA complex that splices out introns.
• It binds to the ends of each EXON and cuts out the introns between them.

Question 16

What is alternative splicing?

Using one recipie bu tweaking ingredients - slightly different cookies

Answer 16

• After the introns are removed, the exons are then rearranged into different combinations and order.
• Enables one single gene to be used to make slightly different proteins

Question 17

Post-transcriptional Modification

What are some other types of Non-coding DNA sequences?

STING - also short tandem repeats

Answer 17

• Satellite DNA
• Telomers
• Introns
• Non-coding RNA genes (codes for RNA that aren’t translated itno proteins - genes for tRNA)
• Gene regulatory sequences

Question 18

Post-transcriptional Modification

Explain the mRNA modificaiton: Five-prime G-caps.

Note: In EUKARYOTES because translation & transcription separate in cell

Answer 18

• Before leaving the nucleus, a G nucleotide is added (triphosate nucleotide)
• Cap provides protection/stability to the mRNA in the cytoplasm where there’s enzymes that can break apart the mRNA.

Question 19

Post-transcriptional Modification

Explain the mRNA modificaiton: Poly A tails

Answer 19

• To protect the 3’ end of mRNA a 100-200 Adenine nucleotide sequence is added.
• If the enzymes in the cytoplasm don’t break off nucelotide, they’ll break off these non-coding As instead of coding sequences of mRNA.

Question 20

Post-transcriptional Modification

Explain mRNA protections for the cytoplasm

mRNA modficiations

Answer 20

• The reason for the addition of a 3’ poly A tail and a 5’ G-cap is because there’s nuclease enzymes in the cytoplasm that degrade mRNA strands that aren’t needed to be translated into proteins.
• Degredation occurs at the 3’ end, so with the tail, it doesn’t impact coding region of mRNA.
• A way of regulations of gene expression

Question 21

Post-transcriptional Modification

Explain the alternative splicing of the toponin T gene.

TPM1 gene makes the protein Toponin (used in muscle contraction)

Answer 21

• For one form of troponin - four different proteins made by the same gene by alternative splicing.
• Two forms made during fetal development, one for healthy adults and a 4th type for diseased hearts.
• Forms made by including/excluding exons 4 & 5 after splicing.

Question 22

Translation

What is translation?

Answer 22

• The process that creates polypeptides at ribosomes
• Involves ‘reading’ the codes on the mRNA and the joining together of amino acids (brought over by tRNA) by peptide bonds.

Question 23

Translation

What is transfer RNA?

tRNA

Answer 23

• Delivers the correct amino acid to the growing polypetide chain.
• tRNAs have anti-codons (complementary to the mRNA CODON that codes for the amino acid the tRNA is caryring) - ensures that the amino acid is dleivered to the correct place.

Question 24

Translation

What is ribosomal RNA?

rRNA subunit

Answer 24

• Strands of RNA that warp around proteins to make the subunits of the ribosomes
• This RNA is structural and doesn’t have a specific function (aside from forming ribosomes)

Question 25

# Translation What is a codon?

Answer 25

* **Every 3 bases of mRNA** * mRNA is read as a triplet code - every 3 bases codes for one amino acid. * Codons are found on mRNA and they determine which amino acid will be added.

Question 26

# Translation What is an Anti-codon? | Note there's uracil in both mRNA and tRNA

Answer 26

* 3 bases on the bottom of the **tRNA** - they tell the tRNA **where to deliver** the amino acid to that is lands on the **correct mRNA codon** * Located on the **tRNA** which DELIVERS the amino acid, whilst the mRNA codon determines WHICH amino acid. * They are **COMPLEMENTARY** to the mRNA codon (complementary to the nucleotide base)

Question 27

# Translation What is the structure of tRNA?

Answer 27

* Complex compared to mRNA, involves **double stranded regions** that form a 'lowercase t shape' with a **single stranded loop** at each point * The bottom of the t is the **3 base anti-codon** and the top of the base is an **attachment place for the amino acid**

Question 28

# Translation What are the two important features of the genetic code to understand?

Answer 28

* It is **UNIVERSAL**: same codons code for same amino acids in every living organism. * It is **DEGENERATE**: because there are 64 codons but only 20 amino acids, **more than ONE codon** codes for **most amino acids** - why some DNA mutations are silent and don't change proteins.

Question 29

# Translation What are the A, P and E sites of the RIBOSOME? | Ribosomes are small = move along mRNA translating as it moves

Answer 29

* At the **A (arrival)**, tRNAs arrive with the amino acid. * It then moves to the **P (peptidly)** site where the amino acid **bonds to the chain** * Then moves to the **E (exit)** site where the tRNA leaves to be reused.

Question 30

# Translation What are the SIX repeating steps that occur in the process of translation? | The steps for each tRNA bringing an amino acid over:

Answer 30

1. tRNA carrying an amino acid **arrives at the A-site** (correct site ensured by anti-codon) 2. That **amino acid forms a peptide bond** to connect it to growing chain 3. tRNA then **shifts to the P site** as ribosome moves down 4. One another tRNA arrives at the A-site, **a new peptide bond forms**, chain shifts to that new tRNA. 5. At that time, **original tRNA shifts** by the ribosomal movement into the **E-site**, leaving the ribosome. 6. That tRNA will have a new amino acid connected and restart.