Question 1

What is the Central Dogma?

Accepted Answer

It states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins.

Question 2

What is a codon?

Accepted Answer

Three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation.

Question 3

What does it mean to be colinear?

Accepted Answer

In terms of RNA and protein, three "units" of RNA (nucleotides) specify one "unit" of protein (amino acid) in a consecutive fashion.

Question 4

What is degeneracy?

Accepted Answer

(of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous.

Question 5

What is a nonsense codon?

Accepted Answer

One of the three mRNA codons that specifies termination of translation.

Question 6

What is a reading frame?

Accepted Answer

A sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein.

Question 7

What is the genetic code?

Accepted Answer

The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and U. Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters. Each amino acid is defined by a three-nucleotide sequence called the triplet codon.

Question 8

What are amino acids?

Accepted Answer

There 20 amino acids used in protein synthesis, each composed of an amino group (NH3+), a carboxyl group (COO–), and a side chain (R). The side chain may be nonpolar/polar, charged/uncharged, small/large, acidic/basic. Variation in amino acid sequence gives rise to enormous variation in protein structure and function.

Question 9

How were codons experimentally demonstrated?

Accepted Answer

Francis Crick and Sydney Brenner used the chemical mutagen proflavin to insert one, two, or three nucleotides into the gene of a virus. When one or two nucleotides were inserted, protein synthesis was completely abolished. When three nucleotides were inserted, the protein was synthesized and functional. This demonstrated that three nucleotides specify each amino acid.

Question 10

Which types of codons have special functions?

Accepted Answer

In addition to instructing the addition of a specific amino acid to a polypeptide chain, three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are called nonsense codons, or stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5' end of the mRNA.

Question 11

How conserved is the genetic code?

Accepted Answer

The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis. Conservation of codons means that a purified mRNA encoding the globin protein in horses could be transferred to a tulip cell, and the tulip would synthesize horse globin. That there is only one genetic code is powerful evidence that all of life on Earth shares a common origin, especially considering that there are about 1084 possible combinations of 20 amino acids and 64 triplet codons.

Question 12

Why is the genetic code degenerate?

Accepted Answer

Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations. Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid but have no effect or specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.

Question 13

What is consensus?

Accepted Answer

A DNA sequence that is used by many species to perform the same or similar functions.

Question 14

What is a core enzyme?

Accepted Answer

A prokaryotic RNA polymerase consisting of α, α, β, and β' but missing σ; this complex performs elongation.

Question 15

What is downstream?

Accepted Answer

Nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3' end relative to a site on the mRNA.

Question 16

What is a hairpin?

Accepted Answer

The structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides

Question 17

What is a holoenzyme?

Accepted Answer

A prokaryotic RNA polymerase consisting of α, α, β, β', and σ; this complex is responsible for transcription initiation.

Question 18

What is an initiation site?

Accepted Answer

A nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction, denoted with a "+1".

Question 19

What is a non-template strand?

Accepted Answer

A strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA.

Question 20

What is a plasmid?

Accepted Answer

Extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes.

Question 21

What is a promoter?

Accepted Answer

A DNA sequence to which RNA polymerase and associated factors bind and initiate transcription.

Question 22

What is Rho-dependent termination?

Accepted Answer

In prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template.

Question 23

What is Rho-independent termination?

Accepted Answer

Sequence-dependent termination of prokaryotic mRNA synthesis caused by hairpin formation in the mRNA that stalls the polymerase.

Question 24

What is a TATA box?

Accepted Answer

A conserved promoter sequence in both eukaryotes and prokaryotes that helps to establish the initiation site for transcription.

Question 25

What is a template strand?

Accepted Answer

A strand of DNA that specifies the complementary mRNA molecule.

Question 26

What is a transcription bubble?

Accepted Answer

A region of locally unwound DNA that allows for transcription of mRNA.

Question 27

What is upstream?

Accepted Answer

Nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA.

Question 28

How do prokaryotic genomes differ from eukaryotes?

Accepted Answer

A bacterial chromosome is a covalently closed circle that, unlike eukaryotic chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is called the nucleoid. In addition, prokaryotes often have abundant plasmids, which are shorter circular DNA molecules that may only contain one or a few genes. Plasmids can be transferred independently of the bacterial chromosome during cell division and often carry traits such as antibiotic resistance.

Question 29

How are downstream and upstream denoted?

Accepted Answer

Downstream nucleotides are denoted with positive (+) numbers and upstream nucleotides are denoted with negative (–) numbers.

Question 30

How is the efficiency of transcription in prokaryotes increased?

Accepted Answer

Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often covers more than one gene and produces polycistronic mRNAs that specify more than one protein.

Question 31

How is the prokaryotic RNA polymerase organized?

Accepted Answer

Prokaryotes use the same RNA polymerase to transcribe all of their genes. In E. coli , the polymerase is composed of five polypeptide subunits, two of which are identical. Four of these subunits, denoted α, α, β, and β' comprise the polymerase core enzyme. These subunits assemble every time a gene is transcribed, and they disassemble once transcription is complete. Each subunit has a unique role; the two α-subunits are necessary to assemble the polymerase on the DNA; the β-subunit binds to the ribonucleoside triphosphate that will become part of the nascent “recently born” mRNA molecule; and the β' binds the DNA template strand. The fifth subunit, σ, is involved only in transcription initiation. It confers transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site. Without σ, the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein gibberish. The polymerase comprised of all five subunits is called the holoenzyme.

Question 32

How do prokaryotic promoters work?

Accepted Answer

In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although promoters vary among prokaryotic genomes, a few elements are conserved. At the -10 and -35 regions upstream of the initiation site, there are two promoter consensus sequences, or regions that are similar across all promoters and across various bacterial species. The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence, TTGACA, is recognized and bound by σ. Once this interaction is made, the subunits of the core enzyme bind to the site. The A–T-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made. The transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10 nucleotides that are made and released.

Question 33

How does transcription elongation occur in prokaryotes?

Accepted Answer

The transcription elongation phase begins with the release of the σ subunit from the polymerase. The dissociation of σ allows the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it. The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely.

Question 34

What are the kinds of termination signals for prokaryotic transcription?

Accepted Answer

Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho protein, Rho-independent termination is controlled by specific sequences in the DNA template strand.

Question 35

How does Rho-dependent termination work?

Accepted Answer

Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.

Question 36

How does Rho-independent termination work?

Accepted Answer

Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C–G nucleotides. The mRNA folds back on itself, and the complementary C–G nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall as soon as it begins to transcribe a region rich in A–T nucleotides. The complementary U–A region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript.

Question 37

What happens on completion of transcription in prokaryotes?

Accepted Answer

Upon termination, the process of transcription is complete. By the time termination occurs, the prokaryotic transcript would already have been used to begin synthesis of numerous copies of the encoded protein because these processes can occur concurrently. The unification of transcription, translation, and even mRNA degradation is possible because all of these processes occur in the same 5' to 3' direction, and because there is no membranous compartmentalization in the prokaryotic cell. In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.

Question 38

What is a CAAT box?

Accepted Answer

(GGCCAATCT) an essential eukaryotic promoter sequence involved in binding transcription factors.

Question 39

What is FACT?

Accepted Answer

Complex that "FAcilitates Chromatin Transcription" by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by.

Question 40

What is a GC-rich box?

Accepted Answer

(GGCG) a nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter.

Question 41

What is an Octamer box?

Accepted Answer

(ATTTGCAT) a nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter.

Question 42

What is a preinitiation complex?

Accepted Answer

A cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template.

Question 43

What is small nuclear RNA (snRNA)?

Accepted Answer

Molecules synthesized by either RNA polymerase II or III that serve a variety of functions, including splicing pre-mRNAs and regulating transcription factors.

Question 44

How does eukaryotic transcription differ from prokaryotic transcription?

Accepted Answer

Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most important difference between prokaryotes and eukaryotes is the latter’s membrane-bound nucleus and organelles. With the genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its mRNA from degrading before it is translated. Eukaryotes also employ three different polymerases that each transcribe a different subset of genes. Eukaryotic mRNAs are usually monogenic, meaning that they specify a single protein.

Question 45

What is required for a eukaryotic RNA polymerase to bind to a DNA template?

Accepted Answer

Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase.

Question 46

What does RNA polymerase I do?

Accepted Answer

RNA polymerase I is located in the nucleolus and synthesizes all of the rRNAs except for the 5S rRNA molecule.

Question 47

What is the nucleolus?

Accepted Answer

A specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes.

Question 48

What does rRNA do?

Accepted Answer

rRNA molecules are considered structural RNAs because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are essential to the process of translation.

15: Genes and Proteins Flashcards

The Genetic Code, Prokaryotic Transcription, Eukaryotic Transcription, RNA Processing in Eukaryotes, Ribosomes and Protein Synthesis

Brainscape's Knowledge GenomeTM

15: Genes and Proteins Flashcards

The Genetic Code, Prokaryotic Transcription, Eukaryotic Transcription, RNA Processing in Eukaryotes, Ribosomes and Protein Synthesis

Brainscape's Knowledge Genome^TM