BIO2: Central Dogma: Transcription and Translation

Question 1

Describe the Central Dogma

Answer 1

Process which proteins are synthesized from genetic code (DNA -> RNA -> protein)

Question 2

Describe transcription

Answer 2

DNA -> RNA: mRNA is synthesized using DNA as a template

Question 3

What synthesizes mRNA from the DNA template?

Answer 3

RNA polymerase

Question 4

Where does DNA transcription occur?

Answer 4

In the nucleus for eukaryotes

Question 5

What is the difference between DNA Pol and RNA Pol?

Answer 5

RNA polymerase does not require a primer, RNA Pol cannot proofread the synthesized RNA (transcription errors are more common than replication errors)

Question 6

What are the steps of transcription?

Answer 6

1. Initiation: RNA Pol and factor sigma form haloenzyme to bind promoter region of DNA
2. Elongation: RNA Pol add free floating nucleotide
3. Termination
4. Regulation of Transcription: through enhancers and repressors

Question 7

Define factor sigma

Answer 7

A helper molecule that binds to the promoter region of the DNA along with RNA polymerase

Question 8

What is the difference between prokaryotic and eukaryotic promoters

Answer 8

Prokaryotic promoters have specific sequences at -10 and -35 (upstream) which bind to RNA Pol. Eukaryotic promoters have “TATA” boxes with many T and A bases

Question 9

Define promoter

Answer 9

A region of the DNA just upstream from the setart site that binds to RNA polymerase and factor sigma to initatie transcription

Question 10

What direction is RNA elongated?

Answer 10

5’ to 3’

Question 11

Describe translation

Answer 11

RNA -> protein: mRNA instructions incode polypeptide formation by ribosomes and tRNA

Question 12

Where does DNA translation occur?

Answer 12

In the cytoplasm

Question 13

Describe codon

Answer 13

3 nucleotides of mRNA that are complementary to the DNA template; each codon codes for a single amino acid

Question 14

Define anticodon

Answer 14

3 nucleotides of tRNA that are complementary to the mRNA codon

Question 15

Describe wobble pairing

Answer 15

Wobble pairing occurs when baes pairing doesn’t follow watson-crick rules (A/T/U, C/G) between codons and anticodons

Question 16

Start codon

Answer 16

AUG (methionine)

Question 17

Stop codon

Answer 17

UAA, UGA, UAG (u are annoying, u go away, u are gone)

Question 18

How many total codons are there?

Answer 18

There are 64 codons total, 3 stop and remaining 61 codons for 20 AAs

Question 19

Define the open reading fram

Answer 19

The continuous stretch of nucleotides that has the possibility of being translated as defined by start/stop codons

Question 20

Describe repressors

Answer 20

Proteins that bind to the promoter region or the silencer regions of DNA to decrease the rate of transcription

Question 21

What is the relationship between RNA Pol and the promoter?

Answer 21

The stronger the affinity between RNA pol and the promoter, the higher the transcription rate

Question 22

Describe enhancers

Answer 22

Enhancers are a region of DNA (usually distant from target gene) that activator proteins bind to to increase the rate of transcription

Question 23

Describe RNA process in eukaryotes

Answer 23

Transcription in eukaryotes produces hnRNA, a precursor to mRNA that is process in the nucleus and mature mRNA is shipped out to be translated

Question 24

Define splicing

Answer 24

Splicing occurs when a splieosome complex removes introns and joins exons

Question 25

Define introns

Answer 25

Introns are regions of a gene that are transcribed but not translated and do not encode proteins but are important to break the gene into distinct exons that contain splice sites that are recognized by the spliceosome

Question 26

Define exons

Answer 26

Exons are regions of a gene that encode the protein sequence (Exons are expressed)

Question 27

What are the components of a spliceosome?

Answer 27

snRNA (small nuclear RNA) + proteins; aka snRNPs (small nuclear ribonucleoproteins)

Question 28

Describe alternative splicing

Answer 28

Alternative splicing skips/splices some exons so that different combinations of exons can make more than 1 different mRNA from the same hnRNA

Question 29

Describe the cap and tail

Answer 29

A 5'cap (methylated guanine) and 3' poly-A tail (multiple adenine nucelotides) is added to the 5' and 3' UTR of the pre-mRNA to increase the mRNA's stability and protect it from degredation in the cytoplasm

Question 30

Define ribozymes

Answer 30

RNA enzymes found in ribosomes which catalyze translation and required for splicing

Question 31

Describe rRNA

Answer 31

rRNA makes up ribosomes which catalyze the synthesis of poly peptides

Question 32

Describe tRNA

Answer 32

tRNA contains anti-codon complementary to mRNA codons and brings the correct amino acid to the growing polypeptide chain due to this codon-anticodon-interaction

Question 33

How is the stem/loop structure in tRNA formed?

Answer 33

Intramolecular H-bonds

Question 34

What is the modified A base in tRNA?

Answer 34

Inosine - often at the wobble position of the anticodon; can pair with A, U, C

Question 35

Describe the composition of ribosome

Answer 35

Ribosomes are composed of rRNA and contain and large and small subunit

Question 36

What is the function of the large ribosomal subunit?

Answer 36

Catalyze the peptidyl transfer

Question 37

What is the function of the small ribosomal subunit?

Answer 37

Recognize and binds to the correct region of the mRNA for translation

Question 38

What are the names eukaryotic and prokaryotic sequences where the small ribosomal subunit binds for translation?

Answer 38

Eukaryotes: Kozak sequence; Prokaryotes: Shine-Dalgarno sequence

Question 39

What are the sedimentation coefficients in prokaryotic and eukaryotic ribosomes?

Answer 39

Prokaryotic (70S) = small (30S) + large (50S) | Eukaryotic (80S) = small (40S) + large (60S)

Question 40

What are the ribosome sites?

Answer 40

Regions of the large ribosomal subunit that the tRNA moves through during protein synthesis (A -> P -> E)

Question 41

Where is the growing polypeptide primarily synthesized?

Answer 41

On the P site of the large ribosomal subunit

Question 42

What direction is the polypeptide formed?

Answer 42

mRNA reads 5' -> 3'; therefore polypeptide is made from the N-terminus to c-terminus

Question 43

What is the difference between prokaryotic and eukaryotic translation?

Answer 43

Prokaryotes have polycistronic mRNA and lack of RNA processing allows transcription and translation to occur at the same time

Question 44

How is energy provided to each step in translation?

Answer 44

1. Initiation: initiator proteins (eIF) + small subunit associate with Kozak sequence on mRNA --> scan for start codon --> large ribosomal subunit joins 2. Elongation: Elongation factor and GTP 3. Termination: Release factor and GTP

Question 45

What are the energy requirements for termination of translation?

Answer 45

#AA*4 = #ATP needed

Question 46

How is tRNA loading initiated?

Answer 46

tRNA and AA attachment is a non-spontaneous process which requires 2 ATP/AA (ATP--> AMP)

Question 47

What is the function of aminoacyl tRNA synthetase?

Answer 47

Aminoacyl tRNA synthetase attaches the correct AA to the correct tRNA with high specificity