Gene Expression: The Flow of Information from DNA to RNA to Protein II

Transcription is the process by which the polymerization of __________ guided by complementary base pairing produces an RNA transcript of a gene

State and explain the three steps of transcription in bacterial cells

In the transcription process, the enzyme ____ _______ catalyzes transcription. DNA sequences near the beginning of genes, called _______, signal RNA polymerase where to begin transcription. Most bacterial gene promoters have almost ______ nucleotide sequences in each of two short regions. These are the sites at which RNA polymerase makes particularly _____ contact with the promoters

RNA polymerase adds nucleotides to the growing RNA polymer in the _______ direction. The chemical mechanism of this nucleotide adding reaction is similar to the formation of _________ bonds between nucleotides during DNA replication with one exception (which is?)

_________ of the high-energy bonds in each ribonucleotide triphosphate provides the energy needed for elongation

Seqeunces in the RNA products, known as ________, tell RNA polymerase where to stop transcription

A eukaryotic ___ _____ ___ transcribes genes that encode proteins. The fig illustrates the general structure of the DNA regions of euk. genes that allow ___ ______ ___ to initiate transcription

A key difference with prok is that sequences called _______ that can be thousands of base pairs away from the promoters are often also required for the efficient transcription of euk genes

The AIDS virus uses an exceptional form of transcription, known as _______ _________, to construct a double strand of DNA from an RNA template

The result of transcription is a single strand of RNA known as a ______ ___________. In prokaryotic organisims, the RNA produced by transcription is the actual _____ that guides protein synthesis

In euk organisms, by contrast, most primary transcripts undergo _____ _______ in the nucleus before they migrate to the cytoplasm to direct synthesis. This processing has played a fundamental role in the evolution of ________ organisms

Some RNA processing in eukaryotes modifies only the 5' or 3' ends of the _______ _______, leaving the info content of the rest of the mRNA untouched

Why is the content of the mature mRNA  related but not identical to the complete set of DNA nucleotide pairs in the original gene?

The nucleotide at the 5' end of a euk mRNA is a G in ________ orientation from the rest of the molecule; it is connected through a ___________ linkage to the first nucleotide in the primary transcript

The backward G is not ________ from DNA. Instead, a special ______ enzyme adds it to the primary transcript after __________ of the trasncript's first few nucleotides

Enyzmes known as ______ ________ then add methyl (-CH3) groups to the backward G and to one or more of the succeeding nucleotides in the RNA, forming a so called ________ _____

The gene for collagen (an abundant ______ in connective tissue) has two introns. By contrast, the dystrophin gene has more than 80 introns; the mean intron lenght is 35 kb, but one intron is an amazing _____ kb long

The introns range from ____ bp to over ____ kb. Exons in contrast, vary in size from about ___ bp to a few kilobases

The greater size variation seen in introns compared to exons reflects which 2 facts:
(result?)

Mature mRNAs must contain all of the ______ that are translated into amino acid, including the ______ and ______ codons

In addition, mature mRNAs have sequences at their 5' and 3' ends that are not translated, but still play important roles in regulating the efficiency of translation. They are called  __________ regions, and are located just after the _________ _____ and just before the _______ _______, respectively 

Besides the cap and tail themselves, all of the sequences in a mature mRNA, including all of the codons and both UTRs, must be ________ from the gene's exons

Introns can interrupt a gene at any location, even between the _______ making up a single codon. In such a case, the three nucleotides of the codon are present in two different (but ________) exons

How do cells make a mature mRNA from a gene whose coding sequences are interrupted by introns?

RNA splicing

Why must a gene have one more exon than it does introns?

To construct the mature mRNA, splicing must be remarkably ________. For example, if an intron lies within a codon, splicing must _______ the intron and _________ the codon without disrupting the _______ _______ of the mRNA

Three types of short sequences within the primary transcript (purpose?)

These sites make it possible to sever the the connections between an ______ and the _____ that precede and follow it, and then to join the formerly distant _______

The mechanism for the two sequential cuts in the primary transcript (4-story)

Splicing normally requires a complicated intranuclear machine called the ________, which ensures that all of the splicing reactions take place in concert

The spliceosome consists of four subunits known as ______ ______ ___________. Each of which contains one or two ______ ______ ________ 100 - 300 nucleotides long, associated with proteins in a discrete particle

Certain snRNAs can _____ _____ with the splice donor and splice acceptor sequences in the ________ _________, so these snRNAs are particularly important in bringing together the two exons that flank an intron

Given the complexities of spliceosome structure, it is remarkable that a few primary transcripts can splice them selves without the aid of spliceosome or any additional factor. These rare primary transcripts function as _________ (define)

Sometimes RNA splicing joins together the _____ ______ and ______ _______ at the opposite ends of an intron, resulting in ______ of the intron and _______ of the two successive and now adjacent exons

Alternative splicing produces different ______ molecules that may encode related ______ with different, though partially overlapping, ____ _____ sequences and functions

In effect then, alternative splicing can tailor the nucleotide sequence of a primary transcript to produce more than one kind of _________. _______ ______ largely explains how the 25,000 genes in the human genome can encode the hundreds of thousands of different _________ estimated to exist in human cells

Translation takes place on _______ that coordinate the movements of _______ ______ carrying specific amino acids with the genetic instructions of an mRNA

No obvious chemical _______ or ______ exists between the nucleotide triplets of mRNA codons and the amino acids they specify. Rather, transfer RNAs (tRNAs) serve as _______ molecules that mediate the transfer of info from ______ _____ to _____

Transfer RNAs are _____, _____-stranded RNA molecules 74-95 nucleotides in length.

Several of the nucleotides in tRNAs contain _______ bases produced by chemical alterations of the principal A, G, C, and U nucleotides. Each tRNA carries one particular ______ _____, and all cells must have at least one _______ for each of the common 20 amino acids specified by the genetic code. The name of a tRNA reflects the _____ _____ it carries

The three levels of the structure of tRNAs

At the bottom end of the L, the tRNA carries an _________ (define)

The anticodon _____ forms base pairs with other regions of the tRNA, it is ______ available for base pairing with its complementary mRNA codon

As with other complementary base sequences, during pairing at the ribosome, the strands of anticodon and codon run ________ to each other.

At the other end of the L, where the 5' and 3' ends of the tRNA strand are found, enzymes known as ___________-_______ _________ connect the tRNA to the amino acid that corresponds to the anticodon

These aminoacyl-tRNA synthetases are extraordinarily specific (explain)

Aminoacyl-tRNA synthetases are, the only molecules that read the languages of both _____ _____ and ______. Thus they are the actual molecular ________

Normally, one ________-____ ________ exists for each of the the 20 common amino acids. Each _______ functions with only one amino acid, but the enzyme may recognize several different ______ specific for that amino acid

The figure illustrates the _____-step process that establishes the ______ bond between an amino acid and the 3' end of its corresponding tRNA

A tRNA covalently coupled to its amino acid is called a ______ _______. The bond between the amino acid and tRNA contains substantial energy that is later used to drive _______ bond formation

While attachment of the appropriate amino acid charges a tRNA, the amino acid itself does not play a _______ role in determining where it becomes incorporated in a growing polypeptide chain. Instead, the specific interaction between a ______ _______ and an _____ _______ make the decision

Although at least one kind of tRNA exists for each of the 20 common amino acids, cells do not necessarily carry tRNAs with anticodons that are  ___________ to all of the 61 possible codon triplets in the genetic code. E. coli, for example, makes 79 different tRNAs containing 42 different anticodons. Although several of the 79 tRNAs in this collection obviously have the same anticodon, 61-42=19 of the 61 potential ________ are not represented

Thus 19 mRNA codons will not find a _________ anticodon in the E. coli collection of tRNAs.

How can an organism construct proper polypeptides if some of the codons in its mRNAs cannot locate tRNAs with complementary anticodons?

Francis Crick spelled out some rules of base pairing between codons and anticodons. He reasoned that the 3' nucleotide in many codons adds ______ to the specificity of the codon. For example, 5' GGU 3', 5' GGC 3' all encode glycine.

It does not matter whether the ____ nucleotide in the codon is U, C, A or G as long as the first two letters are GG (for glycine). The same is true for other amino acids encoded by four different codons, such as vaine (GU)

For amino acids specified by two different codons, the first two bases of the codon are, once again, ________ the same, while the third base must be either one of the two ________  or one of the two __________

Thus, 5' CAA 3' and 5' CAG 3' are both codons for glutamine and 5' CAU 3' and 5' CAC 3' are both codons for histidine. If pu stands for either purine and Py stands for either pyrimidine then CAPu represents the codon for ______ and CAPy represents the codons for ________

The 5' nucleotide of a tRNA's anticodon can often pair with more than one kind of nucleotide in the _____ position of an mRNA's codon. Remember, after base pairing the bases in the anticodon run ________ to the bases in the codon.

A single tRNA charged with a particular amino acid can thus recognize _______ or even _____ of the codons for that amino acid. This flexibility in base pairing between the 3' nucleotide in the codon and the 5' nucleotide in the anticodon is known as _______

The combination of normal base pairing at the first two positions of a codon with wobble at the _______ position clarifies why multiple codons for a single amino acid usually start with the same two letters

An important aspect of wobble is the chemical modification of certain bases at the 5' end of the anticodon (the _______ position). An A in the ______ position of a tRNA is always modified to _________, and a U in the wobble position is always modified in one of ______ possible ways.

By contrast, G in the anticodon wobble position is always ________, while modification of C occurs only in the tRNAs of some ________ species. Wobble bases are modified by specific enzymes that act on the tRNA after it has been synthesized by ________

The wobble rules delimit the anticodon sequences and the wobble base modifications that are consistent with the genetic code. For example, methionine (Met) specified by one codon (AUG). Give a detailed explanation of the result

Ribosomes facilitate polypeptide synthesis in various ways. (5) State them

In E. coli, ribosomes consist of ______ different ribosomal RNAs and _____ different ribosomal proteins. These components associate to form two different ribosomal subunits called the _____ subunits and the _____ subunits (with S designating a coefficient of ________ related to the _____ and ______ of the subunit). Which is smaller?

Before translation begins, the two subunits exist as _______ entities in the cytoplasm. Soon after the start of translation, they come together to reconstitute a complete _________. In euks. they have ____ components than their prok counterparts but they still consist of _____ dissociable subunits

The small 30S subunit is the part of the ribosome that initially binds to _____. The larger 50S subunit contributes an enzyme known as ______ _______, which catalyzes formation of the peptide bonds joining adjacent amino acids

Label

Both the small and the large subunits contribute to the three distinct tRNA binding areas knwon as the ________ site , the ________ site and the ______ site.

Finally, other regions of the ribosome distributed over the _____ subunits serve as points of contact for some of the additional proteins that play roles in translation

Fig 8.24
Green:
Red:
Lavender:
Other colors: 

As was the case for transcription, translation consists of three phases (3)

Explain the biochemical basis of colinearity, that is the correspondence between the 5' to 3' direction in the mRNA and the N-terminus to C-terminus direction in the resulting polypeptide (5-story)

Translation story

Shine-Dalgarno box
Kozak sequence

Polyribosome

Protein structure is not irrevocably fixed at the completion of _________. Several different processes may subsequently modify a polypeptide's structure. Cleavage may remove amino acids, such as the N-terminal fMet, from a polypeptide, or it may generate several ________ polypeptides from one ______ product of translation

The larger polypeptide made before it is cleaved into smaller polypeptides is often called a _________. Also some proteins are synthesized in inactive forms called ______ that are activated by enzymatic cleavage that removes an ________ _______

Two reasons why posttransational modifications can be very important.
Name the most important mod