L5. Gene expression & protein synthesis I

Question 1

explain the cellular control of gene expression

Answer 1

• if cell A in an organism needs protein A, it will make a lot of transcripts for protein A, upregulating it, but not a lot of protein B, deregulating it
• if cell B in the same organism needs protein B, it will up regulate protein B while deregulating protein A

Question 2

cellular control of gene expression - stem cells

Answer 2

• cells that can differentiate into different kinds of cell
• can do this through up regulation and deregulation of certain proteins

Question 3

define transcription

Answer 3

an ongoing process which occurs in many places at the same time (even for the same gene)

Question 4

how is RNA different from DNA

Answer 4

• single strand
• U instead of T
• ribose sugar

Question 5

how is DNA different from RNA

Answer 5

• double strand
• T instead of U
• deoxyribose sugar

Question 6

DNA - what is the coding strand

Answer 6

• oriented in a 5’ to 3’ fashion
• looks like the finished mRNA

Question 7

DNA - what is the template strand

Answer 7

• oriented in a 3’ to 5’ fashion
• strand that is used to make the mRNA

Question 8

explain the intramolecular base-pairing of RNA

Answer 8

• RNA is not linear, it may go conventional or nonconventional base pairings
• it can form 3D structures to allow things to bind to it and interact with it
• these structures all have different functions

Question 9

intermolecular base-pairing of RNA - conventional vs nonconventional base pairing

Answer 9

• conventional base pairing: A-U, G-C
• nonconventional: G-U, C-A

Question 10

explain how RNA polymerase carries out transcription

Answer 10

• since DNA is not hydrogen bounded, it can be easily displaced and allow the RNA pol to transcript the code
• RNA pol uses mRNA molecules from 5’ to 3’
• to begin translation, it jumps onto the promoter region and recognizes the start codon

Question 11

how is RNA pol different from DNA pol

Answer 11

• uses ribonucleotides
• doesn’t need a primer for transcription
• does not have the capacity for proofreading
• more mistakes

Question 12

how is DNA pol different than RNA pol

Answer 12

• uses dNTPs
• needs primers for transcription
• does have the capacity for proofreading
• less mistakes

Question 13

RNA pol vs DNA pol - why did RNA pol evolve to be mistake prone and DNA pol did not

Answer 13

• if there is a mutation in an mRNA, the mutation will be passed onto a small number of proteins
• if there is a mutation in DNA, then the mistake impacts the whole cell and thus all of the protein
• so its less dangerous if there is a mutation in RNA

Question 14

explain the types of RNA molecules

Answer 14

• messenger RNAs (mRNAs)
• ribosomal RNAs (rRNAs)
• microRNAs (miRNAs)
• transfer RNAs (tRNAs)
• other noncoding RNAs

Question 15

types of RNA - mRNA function

Answer 15

code for proteins

Question 16

types of RNA - rRNA function

Answer 16

• form the core of the ribosome’s structure
• catalyze protein synthesis

Question 17

types of RNA - miRNA function

Answer 17

regulate gene expression

Question 18

types of RNA - tRNA function

Answer 18

serve as adaptors between mRNA and amino acids during protein synthesis

Question 19

types of RNA - other noncoding RNA function

Answer 19

• used in RNA splicing
• gene regulation
• telomere maintenance
• many other processes

Question 20

explain transcription in bacteria

Answer 20

bc there is no nucleus, transcription of mRNA and translation into a protein can happen at the same time

Question 21

bacterial transcription - sigma factor

Answer 21

• recognizes promoter region and tells RNA pol to make mRNA
• it zips along the DNA (without unwinding it) with RNA pol until is encounters a promoter region
• then mRNA is made

Question 22

bacterial transcription - promoter

Answer 22

• tells RNA pol to make mRNA
• has certain repeat sequences
• it is upstream of the starting point for RNA synthesis
• it will not be in the mRNA when transcription is done

Question 23

how can genes be transcribed in different directions

Answer 23

• polymerases can use either on of the DNA strands as a template
• the promoter is always near the 3’ end and transcription occurs in the opposite direction towards 5’

Question 24

how is prokaryotic RNA pols different than eukaryotic pols

Answer 24

• 1 RNA pol
• not a lot of regulatory elements
• genes are closer together
• RNA pol and sigma factor initiates transcription

Question 25

how is eukaryotic RNA pols different than prokaryotic RNA pols

Answer 25

- 3 RNA pols - RNA pols need accessory proteins: general transcription factors - transcription initiation is more complicated - many regulatory sequences, more complex regulation, genes further apart - transcription has to take into account DNA packaging (nucleosomes)

Question 26

eukaryotic transcription - RNA pol I

Answer 26

transcribes most rRNA genes

Question 27

eukaryotic transcription - RNA pol II

Answer 27

transcribes: - all protein-coding genes - miRNA genes - plus genes for noncoding RNAs

Question 28

eukaryotic transcription - RNA pol III

Answer 28

transcribes: tRNA genes, 5S rRNA gene, and genes for many other small RNAs

Question 29

explain eukaryotic transcription

Answer 29

- first, a transcription factor needs to find the TATA box (the promoter region) - another transcription factor will recruit RNA pol to the box - another transcription factor hydrolyzes ATP for energy - another transcription factor uses the energy to phosphorylate the pol tail to allow enzymes to bind on it

Question 30

eukaryotic transcription - what enzymes bind on the pol tail

Answer 30

- enzymes for capping, splicing, and polyadenylation - the polyadenylation signal, signals the end of transcription

Question 31

eukaryotic transcription - explain RNA processing

Answer 31

- RNA as to be processed before leaving the nucleus - to leave the nucleus, it has to have a 5' cap and a poly-A tail

Question 32

eukaryotic transcription: mRNA processing - mRNA capping

Answer 32

- this refers to the modification of the mRNA 5' end - the capping results in an addition of a guanine with a methyl group - happens when ~25 nucleotides have been transcribed

Question 33

eukaryotic transcription: mRNA processing - polyadenylation

Answer 33

- first, the 3' end is trimmed by an enzyme - next, a second enzyme adds a series of repeated adenines - happens after the noncoding sequence - this attracts relevant proteins to bind onto the RNA pol II tail

Question 34

eukaryotic genes - introns

Answer 34

- noncoding sequence - cut by splicing factors before final mRNA is released

Question 35

eukaryotic genes - exons

Answer 35

- represented in the open reading frame as coding sequences - splicing factors glue them together after introns are taken out

Question 36

eukaryotic genes - why is it advantageous to have more introns

Answer 36

- alternative splicing - Can splice these in difference combinations and get different functions - different versions of the same protein, made from the same gene, but with different functions

Question 37

explain the splicing process

Answer 37

the spliceosome complex facilitates removal of intron and splicing of exons

Question 37

how is mature mRNA reconigzed

Answer 37

- by RNA-binding proteins - they recognize the 5' cap, poly-A tail, and exon junctions and the mRNA will be exported out of the nucleus

Question 37

splicing process - what is it regulated by

Answer 37

- snRNPs (small nuclear ribonucleic proteins) - they interact with the spliceosome complex and recognizes exon-intron boundaries and removing introns

Question 38

mature mRNA - what happens in the cytosol before translation

Answer 38

protein exchange in which 5' cap binding protein is swapped for translation initiation factors