Chapter 7- RNA and the Genetic Code

Question 1

monocistronic

Answer 1

eukaryotic mRNA is monocistronic, meaning that each mRNA molecule translates into only one protein product.

Question 2

polycistronic

Answer 2

prokaryotic mRNA may be polycistronic, and starting translation at different locations in the mRNA can result in different proteins

Question 3

aminoacyl-tRNA synthetase

Answer 3

different types activate different amino acids, requires 2 ATP

Question 4

start codon

Answer 4

AUG (codes for methionine)

Question 5

stop codon

Answer 5

UAA (U Are Annoying)
UGA (U Go Away)
UAG (U Are Gone)

Question 6

only amino acids with one code

Answer 6

methionine and tryptophan

Question 7

wobble position

Answer 7

third position for codon. usually the first two nucleotides are the same so the third is a variable one. mutations here are typically silent or degenerate mutations.

Question 8

expressed mutations

Answer 8

1. missense: one amino acid substitution

2. nonsense: mutation encodes for a premature stop codon (aka. truncation mutation)

Question 9

TATA Box

Answer 9

promoter region for RNA polymerase II to bind during transcription. typically in -25 for gene location numbering system.

Question 10

2 differences between DNA and RNA polymerases

Answer 10

RNA polymerases don’t require an RNA primer to start generating a transcript and they dont check their work, no editing done.

Question 11

heterogeneous nuclear RNA (hnRNA)

Answer 11

primary transcript and after some modifications it becomes mRNA

Question 12

steps between hmRNA and mRNA? (known as posttranscriptional processing)

Answer 12

1. Intron/exon splicing
2. 5’ cap
3. 3’ poly-A tail

Question 13

intron/exon splicing

Answer 13

spliceosome: made up of small nuclear RNA (snRNA) and small nuclear ribonucleoproteins (snRNPs). these recognize introns and cuts them out to form a lariat (lasso-shaped structure). they are then degraded.
introns- noncoding sequences are removed
exons- coding sequences are ligated

Question 14

alternative splicing

Answer 14

primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene. many more proteins made from limited genes

Question 15

RNA Polymerase I

Answer 15

Synthesizes rRNA

Question 16

RNA Polymerase II

Answer 16

Synthesizes mRNA (and hnRNA)

Question 17

RNA Polymerase III

Answer 17

Synthesizes tRNA and some rRNA

Question 18

3 steps in translation

Answer 18

1. initiation
2. elongation (APE sites)
3. termination

*Note: all steps require energy

Question 19

what happens at the P site for translation (during elongation)

Answer 19

peptide bond forms using peptidyl transferase (enzyme part of the large subunit). GTP used for energy.

Question 20

chaperones

Answer 20

assist in protein folding

Question 21

carboxylation

Answer 21

usually serves as a Ca2+ binding site

Question 22

phosphorylation

Answer 22

usually activates or deactivates a protein

Question 23

operon

Answer 23

cluster of genes transcribed as a single mRNA. 2 types: inducible and repressible systems. offer a simple on-off switch for gene control in prokaryotes.

Question 24

Jacob-Monod Model of an operon

Answer 24

1. regulator gene- codes for repressor protein
2. promoter site- RNA polymerase binding site
3. operator site- nontranscribable and can bind a repressor protein
4. structural gene- codes for protein

Question 25

inducible system (prokaryotes)

Answer 25

repressor bound tightly to operator system so RNA polymerase cannot get to structural gene. inducer must remove the repressor. positive control mechanism b/c repressor is removed from operon by the inducer to promote transcription.

Question 26

1 example of an inducible system (prokaryotes)

Answer 26

lac operon only induced in presence of high lactose and low glucose. assisted by binding of catabolite activator protein (CAP)-starts transcription.

Question 27

negative control mechanism (prokaryotes)

Answer 27

repressible systems. repressor-corepressor complex binds to the operon to prevent transcription.

Question 28

repressible systems (prokaryotes)

Answer 28

allow constant production of a protein. repressor is made by regulator gene in inactive until it binds to a corepressor. then this complex binds to the operator site preventing further transcription. negative control mechanism b/c typically protein being made is the corepressor.

Question 29

1 example of a repressible system (prokaryotes)

Answer 29

trp operon controls manufacturing of tryptophan. when tryptophan is high in local environment it acts as a corepressor.

Question 30

transcription factors

Answer 30

transcription-activating proteins that search DNA for specific DNA-binding motifs. 2 recognizable domains: DNA-binding domain and activation domain.

Question 31

DNA-binding domain

Answer 31

part of transcription factor that binds to specific nucleotide sequence in the promoter region or to a DNA response element (sequence of DNA that binds only to specific transcription factors) to help recruiting transcriptional machinery.

Question 32

activation domain

Answer 32

part of transcription factor that allows for binding of several transcription factors and other regulatory proteins, (ex: RNA polymerase and histone acetylase)

Question 33

2 routes for gene amplification

Answer 33

1. enhancers: several response elements, which allows for control of one gene’s expression by enhancing RNA polymerase at a single promoter site (signal moleule ex: cAMP).
2. gene duplication: can duplicate in series and parallel

Question 34

cis vs. trans regulators

Answer 34

cis: in same vicinity as gene they control
trans: produced and translocated back to the nucleus, travel through cell to their point of action

Question 35

histone acetylation

Answer 35

coactivator that is recruited by transcription factors. involved in chromatin remodeling. acetylation of histone decreases + charge on lysine and open chromatin comformation allowing transcription machines to get to DNA.

Question 36

histone deacetylases

Answer 36

gene silencing. proteins that remove acetyl groups from histones, resulting in closed chromatin formation and decrease in gene expression levels.

Question 37

DNA methylation

Answer 37

DNA methylases add methyl groups to cytosine and adenine nucleotides. this typically silences gene expression.

Question 38

enzymes involved in transcription

Answer 38

1. helicase
2. topoisomerases
   * used to unwind DNA and prevent supercoils
3. RNA polymerase II (main player, binds to TATA box promoter region)