ch.13

transcription factors

In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription. slide 15

What are the similarities and differences between DNA and RNA polymerases?

SIMILARITIES: -Like the DNA polymerases, an RNA polymerase can only perform template-directed synthesis in the 5′ to 3′ direction. -Like the DNA polymerases, an RNA polymerase can only perform template-directed synthesis in the 5′ to 3′ direction. DIFFERENCES: -Unlike DNA polymerases, RNA polymerases DO NOT require a primer to begin synthesis. slide 13

Be able to explain how RNA processing works. Does it occur in prokaryotes and eukaryotes? What is pre-mRNA? What is RNA splicing? What are introns and exons? What is a poly(A) tail?

Specific enzymes are involved in the RNA processing that produces a mature mRNA: Certain interior sections of the pre-mRNA are cut out and the remaining sections are spliced together. Both ends of the pre-mRNA are altered. Eukaryotes In eukaryotes, the product of transcription is an immature primary transcript, or pre-mRNA. Before primary transcripts can be translated, they have to be processed in a complex series of steps. slide 18 The transcription of eukaryotic genes by RNA polymerase generates a primary RNA transcript (pre-mRNA) that contains exons and introns. Introns are removed by splicing. 20 Exons are the coding regions of eukaryotic genes that will be part of the final mRNA product. The intervening noncoding sequences are called introns, and are not in the final mRNA. slide 19 The poly-A tail extends the life of an mRNA by protecting it from degradation. slide 22

Why did Francis Crick propose the 'wobble' hypothesis? Explain this hypothesis.

The tRNA anticodon CCG can match the mRNA codons GGC and GGU because the third position does not affect which amino acid is coded (both code for Gly).

What are polyribosomes and how do they work?

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Compare RNA polymerase in bacteria and eukaryotes.

DURING TERMINATION In bacteria, there is a terminator sequence in the DNA that causes the RNA polymerase to detach from the DNA and release the mRNA transcript. In eukaryotes, RNA polymerase transcribes a sequence on the DNA called the polyadenylation signal sequence, which codes for a polyadenylation signal (AAUAAA) in the mRNA transcript. slide 17

What is mRNA? Explain how it is constructed by describing the three stages of transcription.

The RNA strand built to be complementary to the template strand is called messenger RNA (mRNA slide 10

What are some potential functions of introns?

-Some introns might contain sequences that regulate gene expression or affect gene products. -An important consequence of the presence of introns in genes is that a single gene can encode more than one kind of polypeptide. slide 21

Initiation

-first stage of transcription: -RNA polymerase begins transcription by prying the two strands of DNA apart and synthesizing the mRNA strand based on the template strand. Elongation is the second stage of transcription: slide 12

How many amino acids are there? How can four DNA bases encode so many amino acids? What is a codon?

20 The instructions for a polypeptide are written in the DNA as a series of non-overlapping, three-nucleotide words (triplets), called codons. slide 8

Describe the three step cycle of polypeptide chain elongation. Which steps require energy expenditure in the form of GTP hydrolysis?

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Elongation

Elongation is the second stage of transcription: During the elongation phase of transcription, RNA polymerase moves along the DNA template and synthesizes RNA in the 5' 3' direction. slide 16

Why are tRNAs referred to as translators?

Francis Crick first proposed that an adapter molecule holds amino acids in place while interacting directly and specifically with a codon in mRNA. The adapter molecule was later found to be a small RNA called transfer RNA (tRNA) 24 tRNAs are transcribed from DNA templates, like mRNA, thus they are made in the nucleus. They travel out of the nucleus to the cytoplasm where translation occurs. 25

What is gene expression?

Gene expression is the process by which DNA directs the synthesis of proteins or RNA molecules slide 3

Describe how protein synthesis is a 'change in language'.

In protein synthesis - DNA monomers must be transcribed then translated into protein monomers

promoters

Promoters are specific DNA sequences that come before the start point of transcription (i.e. upstream of the transcription site). RNA polymerase binds in a precise location and orientation on the promoter, which determines where transcription starts and which of the two strands of the DNA helix is used as the template. slide 14

Explain the location and role of RNA polymerase, promoters, and transcription factors in transcription.

RNA polymerase begins transcription by prying the two strands of DNA apart and synthesizing the mRNA strand based on the template strand. (initiation) slide 12

Why do tRNAs have the conformation/structure that they do? How is the shape of tRNAs related to aminoacyl-tRNA synthetase behavior? Where are tRNAs made?

The characteristic 3-dimensional shape of tRNAs is an upside-down L Each tRNA binds to its amino acid at one end (amino acid attachment site) The other end of the tRNA consists of an anticodon, which base-pairs with a complementary codon on mRNA Each tRNA molecule is used repeatedly, picking up its designated amino acid in the cytosol and depositing it along the growing polypeptide chain at the ribosome. 24 25 Enzymes called aminoacyl-tRNA synthetases correctly match tRNAs and amino acids. The active site of each aminoacyl tRNA synthetase fits only a specific combination of amino acid and tRNAs. 27

What are start and stop codons used for? How do they work?

The codon AUG is the start codon that initiates translation, the specific initiator tRNA carries the corresponding amino acid -- methionine 33 A release factor, a protein shaped like a 'charged' tRNA binds directly to the stop codon in the A site, causing the addition of a water molecule instead of an amino acid - this hydrolyzes the chain, releasing the polypeptide through the exit tunnel of the large ribosomal subunit and then the mRNA is released. 36

What role does RNA play in transcription and translation?

The first step in converting genetic information into proteins is transcription - the synthesis of an RNA version of the instructions stored in DNA. The DNA strand to be transcribed is called the template strand The RNA strand built to be complementary to the template strand is called messenger RNA (mRNA) Note: mRNA uses uracil (U) in place of thymine (T) RNA polymerase slide 10

Compare protein synthesis in prokaryotes and eukaryotes.

Transcription and translation occurs in all organisms. The basic mechanisms for transcription and translation are similar for bacteria and eukaryotes with one major difference: The lack of a nuclear membrane in prokaryotic cells means that transcription and translation is not separated in space and time in bacterial cells - translation of mRNA may begin while it is still being transcribed. slide 6

What is a 'charged' tRNA?

When the amino acid is bonded to the tRNA it is called an aminoacyl tRNA or charged tRNA 27

Termination

last stage transcription differs in pro vs euk In bacteria, there is a terminator sequence in the DNA that causes the RNA polymerase to detach from the DNA and release the mRNA transcript. In eukaryotes, RNA polymerase transcribes a sequence on the DNA called the polyadenylation signal sequence, which codes for a polyadenylation signal (AAUAAA) in the mRNA transcript. slide 17