Chapter 7: RNA and the Genetic Code

Question 1

In eukaryotes, mRNA is ______________, meaning that each mRNA molecule translates into only one protein product.

Answer 1

Monocistronic

Question 2

mRNA is the only type of RNA that contains information that is translated into proteins; to do so, it is read in three-nucleotide segments termed ___________.

Answer 2

Codons

Question 3

In prokaryotes, mRNA may be _______________, and starting the process of translation at different locations in the mRNA can result in different proteins.

Answer 3

Polycistronic

Question 4

_____________ (_______) is responsible for converting the language of nucleic acids to the language of amino acids and peptides.

Answer 4

Transfer RNA (tRNA)

Question 5

Mature tRNA is found in the ______________.

Answer 5

Cytoplasm

Question 6

Each type of amino acid is activated by a different __________________ that requires 2 high-energy bonds from ATP (ATP -> AMP), implying that the attachment of the amino acid is an energy rich bond.

Answer 6

Aminoacyl-tRNA synthetase

Question 7

_______________ (_______) is synthesized in the nucleolus and functions as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm.

Answer 7

Ribosomal RNA (rRNA)

Question 8

Many rRNA molecules function as _____________; that is, enzymes made of RNA molecules instead of peptides.

Answer 8

Ribozymes

Question 9

There are a total of _______ codons.

Answer 9

64 codons

Question 10

The genetic code is _________________, in that each codon is specific for one and only one amino acid.

Answer 10

Unambiguous

Question 11

Every preprocessed eukaryotic protein starts with the exact same amino acid: _____________.

Answer 11

Methionine

Question 12

The codon for methionine (_______) is considered the start codon for translation of the mRNA into protein.

Answer 12

AUG

Question 13

There are no charged tRNA molecules that recognize these codons, which leads to the release of the protein from the ribosome. The 3 stop codons are _______, _______, and _______.

Answer 13

• UGA
• UAA
• UAG

Question 14

Stop codons:
- UAA = ______________
- UGA = ______________
- UAG = ______________

Answer 14

• UAA: U Are Annoying
• UGA: U Go Away
• UAG: U Are Gone

Question 15

The genetic code is ______________ because more than one codon can specify a single amino acid.

Answer 15

Degenerate

Question 16

We can see that for the amino acids with multiple codons, the first two bases are usually the same, and the third base in the codon is variable. We refer to this variable third base in the codon as the _______________.

Answer 16

Wobble position

Question 17

Mutations in the wobble position tend to be called ___________ or _____________, which means there is no effect on the expression of the amino acid and therefore no adverse effects on the polypeptide sequence.

Answer 17

• Silent
• Degenerate

Question 18

If a mutation occurs and it affects one of the nucleotides in a codon, it is known as a _______________.

Answer 18

Point mutation

Question 19

Other point mutations can have a severe detrimental effect depending on where the mutation occurs in the genome. Because these point mutations can affect the primary amino acid sequence of the protein, they are called _________________.

Answer 19

Expressed mutations

Question 20

Expressed point mutations fall into 2 categories: ____________ and ____________.

Answer 20

• Missense
• Nonsense

Question 21

_________________ is a mutation where one amino acid substitutes for another.

Answer 21

Missense mutation

Question 22

________________ is a mutation where the codon now encodes for a premature stop codon (also known as a _________________).

Answer 22

• Nonsense mutation
• Truncation mutation

Question 23

Point mutations occur when one nucleotide is changed, but a _________________ occurs when some number of nucleotides are added to or deleted from the mRNA sequence.

Answer 23

Frameshift mutation

Question 24

Transcription results in a single strand of mRNA, synthesized from one of the two nucleotide strands of DNA called the template strand (or the _____________ strand).

Answer 24

Antisense strand

Question 25

RNA is synthesized by a DNA-dependent RNA polymerase; RNA polymerase locates genes by searching for specialized DNA regions known as _______________.

Answer 25

Promoter regions

Question 26

In eukaryotes, _________________ is the main player in transcribing mRNA, and its binding site in the promoter region is known as the TATA box, named for its high concentration of thymine and adenine bases.

Answer 26

RNA polymerase II

Question 27

________________ help the RNA polymerase locate and bind to the TATA box in the promoter region of the DNA, helping to establish where transcription will start.

Answer 27

Transcription factors

Question 28

_________________ does not require a primer to start generating a transcript.

Answer 28

RNA polymerase

Question 29

In eukaryotes: _______________ is located in the nucleolus and synthesizes rRNA.

Answer 29

RNA polymerase I

Question 30

In eukaryotes: _______________ is located in the nucleus and synthesizes hnRNA (pre-processed mRNA) and some small nuclear RNA (snRNA).

Answer 30

RNA polymerase II

Question 31

In eukaryotes: __________________ is located in the nucleus and synthesizes tRNA and some rRNA.

Answer 31

RNA polymerase III

Question 32

The coding strand (or ________________) of DNA is not used as a template during transcription.

Answer 32

Sense strand

Question 33

The primary RNA transcript formed after the termination of transcription is termed ___________________ RNA (_________).

Answer 33

Heterogeneous nuclear RNA (hnRNA)

Question 34

Posttranscriptional processing of hnRNA: - ____________ - ____________ - ____________

Answer 34

- Splicing - 5' cap - 3' poly-A tail

Question 35

Splicing is accomplished by the _______________.

Answer 35

Spliceosome

Question 36

In the spliceosome, _______________ RNA (________) molecules couple with proteins known as ____________________ (also known as ___________, or "slurps").

Answer 36

- Small nuclear RNA (snRNA) - Small nuclear ribonucleoproteins (snRNPs)

Question 37

The noncoding sequences are excised in the form of a ___________ (lasso-shaped structure) and then degraded.

Answer 37

Lariat

Question 38

At the 5' end of the hnRNA molecule, a ______________________ cap is added. It protects the mRNA from degradation in the cytoplasm.

Answer 38

7-methylguanylate triphosphate cap

Question 39

A _____________ (________) tail is added to the 3' end of the mRNA transcript and protects the message against rapid degradation when exiting the nucleus.

Answer 39

Polyadenosyl (poly-A) tail

Question 40

For some genes in eukaryotic cells, the primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene. This process is known as ________________.

Answer 40

Alternative splicing

Question 41

Once the mRNA transcript is created and processed, it can exit the nucleus through ________________.

Answer 41

Nuclear pores

Question 42

The ____________ is composed of proteins and rRNA.

Answer 42

Ribosome

Question 43

There are 3 binding sites in the ribosome for tRNA: the A site (_____________), P site (_____________), and E site (_________).

Answer 43

- Aminoacyl - Peptidyl - Exit

Question 44

_____________ ribosome contains 50S and 30S subunits, which assemble to create the complete 70S ribosome.

Answer 44

Prokaryote

Question 45

______________ have 5S, 23S, and 16S rRNA.

Answer 45

Prokaryotes

Question 46

_____________ ribosome contains 60S and 40S subunits, which assemble to create the complete the complete 80S ribosome.

Answer 46

Eukaryote

Question 47

_________________ have 5S, 5.8S, 28S, and 18S rRNA.

Answer 47

Eukaryotes

Question 48

The process of translation occurs in 3 stages: - _____________ - _____________ - _____________

Answer 48

- Initiation - Elongation - Termination

Question 49

In prokaryotes, the small subunit binds to the ____________________ in the 5' untranslated region (UTR) of the mRNA.

Answer 49

Shine-Dalgarno sequence

Question 50

The small ribosomal subunit binds to the mRNA. The large subunit then binds to the small subunit, forming the completed initiation complex. This is assisted by _______________ (______) that are not permanently associated with the ribosome.

Answer 50

Initiation factors (IF)

Question 51

During elongation: The __________ holds the incoming aminoacyl-tRNA complex. This is the next amino acid that is being added to the growing chain, and is determined by the mRNA codon within the site.

Answer 51

A site

Question 52

During elongation: The _________ holds the tRNA that carries the growing polypeptide chain. It is also where the first amino acid (methionine) binds because it is starting the polypeptide chain.

Answer 52

P site

Question 53

A peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site. This requires _______________, an enzyme that is part of the large subunit. GTP is used for energy during bond formation.

Answer 53

Peptidyl transferase

Question 54

During elongation: The __________ is where the now inactivated (uncharged) tRNA pauses transiently before exiting the ribosome.

Answer 54

E site

Question 55

______________ (_____) assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used.

Answer 55

Elongation factor (EF)

Question 56

When any of the three stop codons moves into the A site, a protein called ______________ (RF) binds to the termination codon, causing a water molecule to be added to the polypeptide chain.

Answer 56

Release factor (RF)

Question 57

The addition of the water molecule to the polypeptide chain allows peptidyl transferase and _______________ to hydrolyze the completed polypeptide chain from the final tRNA.

Answer 57

Termination factors

Question 58

One essential step for the final synthesis of the protein is proper folding. There is a specialized class of proteins called ______________, the main function of which is to assist in the protein-folding process.

Answer 58

Chaperones

Question 59

________________ - addition of a phosphate group by protein kinases to activate or deactivate proteins; it is most commonly seen with serine, threonine, and tyrosine in eukaryotes.

Answer 59

Phosphorylation

Question 60

______________ - addition of carboxylic acid groups, usually to serve as calcium-binding sites.

Answer 60

Carboxylation

Question 61

______________ - addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination.

Answer 61

Glycosylation

Question 62

_____________ - addition of lipid groups to certain membrane-bound enzymes

Answer 62

Prenylation

Question 63

By sharing a single common promoter region on the DNA sequence, these genes are transcribed as a group. This type of structure is called an _____________ - a cluster of genes transcribed as a single mRNA.

Answer 63

Operon

Question 64

The __________________ model is used to describe the structure and function of operons. Operons contain structural genes, an operator site, a promoter site, and a regulator gene.

Answer 64

Jacob-Monod model

Question 65

In the Jacob-Monod model, the _____________ gene codes for the protein of interest.

Answer 65

Structural gene

Question 66

In the Jacob-Monod model, upstream of the structural gene is the _______________, a nontranscribable region of DNA that is capable of binding a repressor protein.

Answer 66

Operator site

Question 67

In the Jacob-Monod model, further upstream of the operator site is the _______________, which is similar in function to promoters in eukaryotes: it provides a place for RNA polymerase to bind.

Answer 67

Promoter site

Question 68

In the Jacob-Monod model, further upstream of the promoter site is the ________________, which codes for a protein known as the repressor.

Answer 68

Regulator gene

Question 69

2 types of operon: - _____________ system - _____________ system

Answer 69

- Inducible system - Repressible system

Question 70

In ______________ system, the repressor is bonded tightly to the operator system and thereby acts as a roadblock.

Answer 70

Inducible system

Question 71

Such inducible systems - in which the binding of protein reduces transcriptional activity - are called _____________ control mechanism.

Answer 71

Negative control mechanism

Question 72

To remove the repressor from the operator system in inducible system, an ____________ must bind the repressor protein so that RNA polymerase can move down the gene.

Answer 72

Inducer

Question 73

Inducible systems operate on a principle analogous to __________________ for enzyme activity: as the concentration of the inducer increases, it will pull more copies oof the repressor off of the operator region, freeing up those genes for transcription.

Answer 73

Competitive inhibition

Question 74

_____________ = the binding of a protein to DNA stops transcription

Answer 74

Negative control

Question 75

______________ = the binding of a protein to DNA increases transcription

Answer 75

Positive control

Question 76

_______________ - the system is normal "off" but can be made to turn "on", given a particular signal.

Answer 76

Inducible system

Question 77

_________________ - the system is normally "on" but can be made to turn "off", given a particular signal.

Answer 77

Repressible system

Question 78

The lac operon is a _________________ system.

Answer 78

Negative inducible system

Question 79

The trp operon is a _________________ system.

Answer 79

Negative repressible system

Question 80

Bacteria only use the lac operon if ____________ is high and ____________ is low.

Answer 80

- Lactose is high - Glucose is low

Question 81

In lac operon, ____________ acts as an inducer.

Answer 81

Lactose

Question 82

The lac operon is assisted by binding of the _____________________ (_______). It is a transcriptional activator used by E. coli when glucose levels are low to signal that alternative carbon sources should be used.

Answer 82

Catabolite activator protein (CAP)

Question 83

In the lac operon, falling levels of glucose cause an increase in the signalling molecule cyclic AMP (cAMP), which binds to __________________ (______). This induces a conformation change in _______ that allows it to bind the promoter region of the operon, further increasing transcription of the lactase gene.

Answer 83

Catabolite activator protein (CAP)

Question 84

________________ allow constant production of a protein product.

Answer 84

Repressible system

Question 85

The repressor in repressible system made by the regulator gene is inactive until it binds to a ________________.

Answer 85

Corepressor

Question 86

Repressible system tend to serve as a _____________. As its level increase, it can bind the repressor, and the complex will attach to the operator region to prevent further transcription of the same gene.

Answer 86

Corepressor

Question 87

The trp operon operates as a _________________ system. When tryptophan is high in the local environment, it acts as a corepressor. The binding of 2 molecules of tryptophan to the repressor causes the repressor two bind to the operator site.

Answer 87

Negative repressible system

Question 88

__________________ are transcription-activating proteins that search the DNA looking for specific DNA-binding motifs.

Answer 88

Transcription factors

Question 89

Transcription factors tend to have 2 recognizable domains: a _______________ domain and an _____________ domain.

Answer 89

- DNA-binding domain - Activation domain

Question 90

The DNA-binding domain of transcription factor binds to a specific nucleotide sequence in the promoter region or to a DNA _________________ (a sequence of DNA that binds only to specific transcription factors.

Answer 90

Response element

Question 91

The ________________ of transcription factor allows for the binding of several transcription factors and other important regulatory proteins, such as RNA polymerase and histone acetylates, which function in the remodelling of the chromatin structure.

Answer 91

Activation domain

Question 92

The DNA regulatory base sequences (such as promoters, enhancers, and response elements) are known as ________ regulators because they are in the same vicinity as the gene they control.

Answer 92

Cis regulators

Question 93

Transcription factors have to be produced and translocated back to the nucleus; thus they are called ________ regulators because they travel through the cell to their point of action.

Answer 93

Trans regulators

Question 94

Response elements outside the normal promoter regions can be recognized by specific transcription factors to enhance transcription levels. Several response elements may be grouped together to form an _____________, which allows for the control of one gene's expression by multiple signals.

Answer 94

Enhancer

Question 95

_____________ regions in the DNA can be up to 1000 base pairs away from the gene they regulate and can even be located within an intron, or noncoding region, of the gene. They differ from upstream promoter elements in their locations because upstream promoter elements must be within 25 bases of the start of a gene.

Answer 95

Enhancer

Question 96

Transcription factors that bind to the DNA can recruit other coactivators such as _________________. These proteins are involved in chromatin remodelling because they acetylate lysine residues found in the amino terminal tail regions of histone proteins.

Answer 96

Histone acetylases

Question 97

______________ of histone proteins decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA, resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA.

Answer 97

Acetylation

Question 98

_______________ are proteins that function to remove acetyl groups from histones, which results in a closed chromatin conformation and overall decrease in gene expression levels in the cell.

Answer 98

Histone deacetylases

Question 99

DNA ______________ add methyl groups to cytosine and adenine nucleotides.

Answer 99

DNA methylases

Question 100

______________ of genes is often linked with the silencing of gene expression. It plays an important role in silencing genes that no longer need to be activated.

Answer 100

Methylation