RNA Synthesis and The Genetic Code

Question 1

mRNA carries the information encoded in the DNA to the ___ where it is ____ into proteins

Answer 1

cytoplasm; translated

Question 2

tRNAs serve as ___ for AAs

Answer 2

carriers

Question 3

rRNA is a major component of the protein synthesizing machinery, the ____

Answer 3

ribosome

Question 4

All RNAs are synthesized by RNA polymerases in the ____. An exception to this is the small percentage of RNA that is synthesized in ____

Answer 4

nucleus; mitochondria

Question 5

True or false? All three classes of RNA require processing of the initial product of transcription to yield a mature RNA molecule

Answer 5

true

note: processing occurs in nucleus

Question 6

Bacteria contains about ____ genes and man perhaps ____ genes.

Answer 6

2000; 25000

Question 7

What are the 5 steps in transcription?

Answer 7

1. location of the segment of DNA to be transcribed (formation of open-promoter complex)
2. synthesis of RNA
3. termination of synthesis
4. processing of the primary transcript
5. prokaryotic vs. eukaryotic

Question 8

Upstream from the transcription start site are sequences of nucleotides called ____ sequences that signal RNA polymerase to bind. This region of DNA is called the ___

Answer 8

consensus; promoter

Question 9

Binding of RNA polymerase to the promoter region causes localized unwinding of the DNA template called an ___ complex

Answer 9

open

Question 10

RNA polymerase is a huge protein, about _____ kDa

Answer 10

500,000

Question 11

RNA synthesis, as with DNA synthesis, proceeds in what direction?

Answer 11

5’ to 3’

Question 12

The RNA polymerase moves along the surface of the DNA in a processive manner. What does this mean?

Answer 12

it stays attached throughout synthesis and elongates the RNA transcript

Question 13

For each of the following RNA polymerase subunits, give its role:
Beta
Beta’
sigma

Answer 13

Beta: active enzyme site
Beta’: important for binding to DNA
sigma: required to recognize and bind to the promoter

Question 14

In regards to the promoter region, 10 residues upstream from the transcription start site is a region known as the ____ box and a second region at -35 rich in __ and ___ known as the -35 region

Answer 14

TATA; A; T

Question 15

Promoter sequences are consensus sequences. What does this mean?

Answer 15

slight variations in sequence may occur between promoters for different genes in these regions

Question 16

RNA polymerase ___ the DNA, opening it into a transcription bubble. Two ribonucleotides enter the bubble and hydrogen bond to the +1 and +2 deoxyribonucleotides of the template strand. A dinucleotide is formed and synthesis has begun. This first stretch of ribonucleotide formed is called the ___.

Answer 16

denatures; primer

note: if this process does not reach 10 nucleotides quickly, transcription will abort

Question 17

In order for RNA polymerase to proceed out of the transcription bubble it must lose the sigma protein. Which protein displaces sigma and also plays a role in efficient elongation of the nascent RNA molecule?

Answer 17

Nus A protein

note: Nus A dissociates at termination step

Question 18

In regards to termination, when a specific base or sequence is copied from the template, RNA synthesis stops. Theses sites posses dyad symmetry and are called ___

Answer 18

palindromes

Question 19

In regards to termination, because the transcribed palindromes can base pair, they form ____ ____, which pull away from the template. When RNA polymers interact with these, transcription stalls.

Answer 19

hairpin loops

Question 20

In ___ independent terminators, there is an adjacent poly A stretch to the hairpin. Poly A-poly U hybrid is very unstable, hence the ____ dissociates from the template

Answer 20

rho; message

Question 21

Rho factor binds to the ___ end of messages as they are being transcribed.

Answer 21

5’

Question 22

When a ribosome “stalls” at a rho termination site, rho factor is able to do what?

Answer 22

“catch up” to the ribosome and termination occurs

Question 23

For each of the following polymerases, give its location, product, and relative activity %:
RNA poly I
RNA poly II
RNA poly III

Answer 23

RNA poly I: nucleolus; rRNA; 50-70%

RNA poly II: nucleoplasm; hnRNA (precursor of mRNA); 20-40%

RNA poly III: nucleoplasm; small RNA (5S RNA, tRNA); 10%

Question 24

___-____ is a toxic compound from certain poisonous mushrooms that inhibit RNA synthesis by RNA polymerase ___

Answer 24

alpha-amanitin; II

Question 25

TATA box directs RNA polymerase to what?

Answer 25

correct start site

Question 26

The CAAT box is present around -__ and is also an important part of the promoter - it controls what?

Answer 26

80; frequency of initiation of transcription

Question 27

mRNA carries the ___ for synthesis of specific proteins.

Answer 27

message

Question 28

In regards to prokaryotes, the message often codes for multiple proteins; this is called being ____. Since there is no nucleus, the message is immediately translated - often when it is still attached to ___

Answer 28

polycistronic; DNA

Question 29

In regards to eukaryotes, the message only codes for one protein, this is called being ____. The sections that carry the necessary code are called ____. The sections which do not carry information for protein synthesis must be removed and are called ____.

Answer 29

monocistronic; exons; introns

Question 30

The prokaryotic mRNA is ___-lived, while the eukaryotic mRNA is ___-lived

Answer 30

short; long

Question 31

mRNA is synthesized in the nucleus as a high molecular weight precursor named ____. This precursor is also always present as a ____

Answer 31

hnRNA (heterogenous nuclear RNA); RNP (protein + RNA)

Question 32

Correct processing of an hnRNA to the mature mRNA is a prerequisite for transport of mRNA to the ___

Answer 32

cytoplasm

Question 33

All hnRNAs and mRNAs contain a structure termed a cap at the __' end of the molecule. The cap consists of what two methylated things?

Answer 33

5; methylated guanine and methylated riboses

Question 34

What is the methyl donor for the methylation reactions forming the 5' cap?

Answer 34

S'-Adenosylmethionine

Question 35

What is the two functions of the cap in eukaryotic mRNA?

Answer 35

1. to protect the 5' end from attack by RNase 2. to permit binding of mRNAs to the 40S ribosomal subunit - without caps, the translation of mRNA is drastically reduced

Question 36

Most hnRNAs contain a sequence of 20-200 adenine residues at the 3' end of the molecule. This stretch of adenine residues is termed the ___(__) tail

Answer 36

poly (A)

Question 37

Not all hnRNAs, and therefore not all mRNAs, contain poly(A) tails at their 3' end. Give an example of an mRNA that doesn't contain a poly(A) tail

Answer 37

mRNA coding for histones

Question 38

What is the function of a poly(A) tail?

Answer 38

to confer stability to the message - messages which have had their tail removed are degraded rapidly

Question 39

When the consensus sequence AAUAAA is read, what does RNA polymerase do?

Answer 39

cleaves the chain followed by addition of poly(A's) at the new 3' end

Question 40

RNA sequences corresponding to the introns are found in what RNAs?

Answer 40

hnRNAs note: means one of the requirements for hnRNA to become mature mRNA is for the introns to be spliced out

Question 41

In regards to the mechanism of splicing mRNA precursors, in all eukaryotic genes, the sequence __ is found where the 5' end of the intron meets the 5' exon

Answer 41

GU

Question 42

In regards to the mechanism of splicing mRNA precursors, the dinucleotide sequence __ marks where the 3' end of the intron joins the 3' exon

Answer 42

AG

Question 43

An adenosine is part of the ___ site (a place important in splicing) and is located approximately 35 nucleotides upstream from the 3' splice site

Answer 43

branch

Question 44

Splicing must be precise. A mutation in the consensus sequence can cause what?

Answer 44

the intron to be retained in the message and result in a nonfunctional protein

Question 45

This is a large protein plus RNA complex (45 protein complexes and 5000 nucleotides of RNA) which catalyzes splicing out the intron.

Answer 45

spliceosome

Question 46

The spliceosome removes the intron by two transesterfication reactions. Where do these transesterfircations take place?

Answer 46

1. between the 5' splice site and a branch-site adenylate | 2. between the 5' exon and the 3' splice site

Question 47

The spliceosome contains a group of proteins that catalyze the transesterfication reactions at the correct sites. What are these proteins called?

Answer 47

SNRPs (small nuclear ribonucleotproteins, "snurps")

Question 48

How many complexes of SNRPs are involved in the formation of a spliceosome?

Answer 48

4

Question 49

Each SNRP comlex is associated with one or more small RNA molecule. List these molecules

Answer 49

U1, U2, U4/6, or U5

Question 50

Catalytic RNA molecules are referred to as ____

Answer 50

ribozymes

Question 51

How does self-splicing occur in lower eukaryotes?

Answer 51

nucleolytic attack by a free GTP molecule on a splice junction which undergoes internal rearrangement to generate the final spliced product

Question 52

Alternative splicing is used to create different mRNA from what?

Answer 52

the same initial hnRNA

Question 53

In Troponin T, alternative splicing allows ___ different isoforms to be created

Answer 53

32

Question 54

What is the function of an intron?

Answer 54

not fully established; maybe protein diversity

Question 55

Since there are 4 nitrogenous bases and 3 code words for an AA, there are ___ possible code words

Answer 55

64 (4^3)

Question 56

How many code words code for AAs and how many code for termination?

Answer 56

61 for AAs; 3 for termination (UAA, UAG, UGA) note: AUG codes for initiation and methionine

Question 57

The base pairing between the codon (in the mRNA) and the anticodon (in the tRNA) is ______

Answer 57

antiparallel

Question 58

The genetic code contains no punctuation - there are no signals required to indicate the end of one codon and the beginning of the next. True or false?

Answer 58

true - therefore it is imperative that translation of the codons in mRNA begin at the correct place

Question 59

The genetic cod is degenerate. What does this mean?

Answer 59

there is more than one code word for most of the amino acids ex: arginine = 6, valine = 4, tryptophan = 1

Question 60

____ indicates that there is less specificity in the third position of the codons than in the first two positions. Therefore base pairing between the codon and anticodon is very specific at the first two positions and not very specific at the third.

Answer 60

wobble

Question 61

The genetic code is almost universal. The various codons code for the same amino acids in all prokaryotic and eukaryotic cells. Exceptions include codons in mito and chloroplasts. True or false?

Answer 61

true

Question 62

The ___ in tRNA is complementary to the codon in the mRNA

Answer 62

anticodon ex: 5' CUA 3' in the codon is matched by 3' GAU 5'

Question 63

For eukaryotes, the spontaneous mutation rate is what?

Answer 63

1 in 10^10 to 1 in 10^11

Question 64

In this type of mutation, a purine is replaced by another purine or pyrimidine is replaced by another pyrimidine

Answer 64

transition

Question 65

In this type of mutation, a purine is changed to a pyrimidine or a pyrimidine is changed to a purine

Answer 65

transversion

Question 66

A mutation that results in a change in codon but no change in AA meaning there is no effect is called what?

Answer 66

silent mutation

Question 67

A mutation that results in alternation of a single base pair in the DNA which leads to insertion of a different AA during protein synthesis is called what?

Answer 67

missense mutation ex: sickle cell disease - a missions mutation might result in a protein of improved function

Question 68

This is the type of mutation that results in the introduction of a stop codon

Answer 68

nonsense mutation

Question 69

Insertions and deletions are _____ mutations, which change the translation of the genetic code for all codons downstream from the mutation

Answer 69

frameshift