Chapter 17: Transcription, RNA processing, & Translation
What is an aminoacyl-tRNA synthetase? What does it do? Understand its structural features - that is, what part attaches to the mRNA and which part holds the amino acid (Fig. 17.12).
Enzymes called aminoacyl tRNA synthetases "charge" the tRNA by Catalyzing the addition of amino acids to tRNAs Aminoacyl tRNAs act as the interpreter in the translation process
What is an intron? An exon?
Exons Are the coding regions of eukaryotic genes Will be part of the final mRNA product Introns are The intervening noncoding sequences Not in the final mRNA
What are basal transcription factors?
General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA.
Name a similarity between RNA polymerase and DNA polymerase? What is a major difference?
Like DNA polymerase an RNA polymerase performs a template-directed synthesis in the 5'>3' direction. But unlike DNA polymerase, RNA polymerases do not require a primer to begin transcription.
Many RNA's (which come from genes) do not code for proteins. Give some examples of other functions that RNA's (which come from genes) perform
Messenger RNA (mRNA) carries the genetic information copied from DNA in the form of a series of three-base code "words," each of which specifies a particular amino acid. Transfer RNA (tRNA) is the key to deciphering the code words in mRNA. Each type of amino acid has its own type of tRNA, which binds it and carries it to the growing end of a polypeptide chain if the next code word on mRNA calls for it. The correct tRNA with its attached amino acid is selected at each step because each specific tRNA molecule contains a three-base sequence that can base-pair with its complementary code word in the mRNA. Ribosomal RNA (rRNA) associates with a set of proteins to form ribosomes. These complex structures, which physically move along an mRNA molecule, catalyze the assembly of amino acids into protein chains. They also bind tRNAs and various accessory molecules necessary for protein synthesis. Ribosomes are composed of a large and small subunit, each of which contains its own rRNA molecule or molecules.
Describe a polyribosome
Multiple ribosomes attached to an mRNA form a polyribosome
What does sigma do?
Sigma Is a protein subunit Must first bind to the polymerase A sigma factor (σ factor) is a regulatory protein needed only for initiation of RNA synthesis. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters.
What is a holoenzyme?
Sigma and RNA polymerase together to form a holoenzyme An enzyme made up of a core enzyme And other required proteins
What is an anticodon?
a set of three ribonucleotides that form base pairs with the mRNA codon.
Define downstream and upstream
DNA that is located in the direction RNA polymerase moves during transcription is said to be downstream from the point of reference; DNA located in the opposite direction is said to be upstream.Thus, the -10 box is centered about 10 bases upstream from the transcription start site. The place where transcription starts is called the +1 site.
The expressed (coding) regions of eukaryotic genes are called ________________?
EXONS
Describe the processing of RNA. Does this occur in bacteria?
In bacteria The information in DNA is converted to mRNA directly In eukaryotes The product of transcription is an immature primary transcript Or pre-mRNA Before eukaryotic primary transcripts can be translated They have to be processed in a complex series of steps The protein-coding regions of eukaryotic genes are interrupted by noncoding regions To make a functional mRNA These noncoding regions must be removed
What is ribosomal RNA (rRNA)?
In molecular biology, ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rRNA and 40% protein by weight.
Describe initiation of transcription?
Initiation is the first phase of transcription RNA polymerase cannot initiate transcription on its own Initiation: RNA polymerase binds to DNA at a specific sequence of nucleotides called the promoter. The promoter contains an initiation site where transcription of the gene begins. RNA polymerase than unwinds DNA at the beginning of the gene.
What is a 5' cap and a poly (A) tail? What is the purpose of the these?
Primary RNA transcripts are also processed by the addition of a 5' cap and a poly(A) tail RNA processing is complete upon Addition of the cap Addition of the poly(A) tail Completion of splicing The product is a mature mRNA The 5' cap serves as a recognition signal for the translation machinery The poly(A) tail extends the life of an mRNA by protecting it from degradation
What are small nuclear ribonucleoproteins (snRNPs)?
RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.
What are promoters?
Sections of DNA that promote the start of transcription. Bacterial promoters Are comprised of 4050 base pairs Have two key regions -10 box and -35 box
What is the A site, P site, & E site?
The A site of the ribosome Is the acceptor site for an aminoacyl tRNA The P site Is where a peptide bond forms that adds an amino acid to the growing polypeptide chain The E site Is where tRNAs no longer bound to an amino acid exit the ribosome
What is the template strand?
The DNA strand read by RNA polymerase ( which is an enzyme) during transcription.
Who is David Pribnow and what was the discovery he made?
The Pribnow box (also known as the Pribnow-Schaller box) is the sequence TATAAT of six nucleotides (thymine-adenine-thymine-etc.) that is an essential part of a promoter site on DNA for transcription to occur in bacteria.[1][2] It is an idealized or consensus sequence—that is, it shows the most frequently occurring base at each position in a large number of promoters analyzed; individual promoters often vary from the consensus at one or more positions. It is also commonly called the -10 sequence, because it is centered roughly 10 base pairs upstream from the site of initiation of transcription. The Pribnow box has a function similar to the TATA box that occurs in promoters in eukaryotes and archaea: it is recognized and bound by a subunit of RNA polymerase during initiation of transcription. This region of the DNA is also the first place where base pairs separate during prokaryotic transcription to allow access to the template strand. The AT-richness is important to allow this separation, since adenine and thymine are easier to break apart (not due to the hydrogen bond count[3]). It is named after David Pribnow and Heinz Schaller.[1][2]
What is the Shine-Delgarno sequence (or ribosome binding site)?
The Shine-Dalgarno (SD) sequence is a ribosomal binding site in prokaryotic messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon.
What is the coding strand?
The non-template strand in DNA, it's sequence matches the sequence of the RNA that is transcribed from the template strand and codes for a polypeptide.
What is a splicosome?
The spliceosome is assembled from snRNAs and protein complexes. The spliceosome removes introns from a transcribed pre-mRNA, a kind of primary transcript.
Describe termination in transcription
Transcription ends with a termination phase RNA polymerase transcribes a transcription termination signal In the DNA template into RNA In bacteria the transcription termination signal Codes for RNA that forms a hairpin structure Causes the RNA polymerase to separate from the RNA transcript Ending transcription
What is transfer RNA (tRNA)? What does it do?
Transfer RNA (or abbreviated as tRNA) is small RNA molecule, typically between 70 to 90 nucleotides in length, which main function is to deliver amino acids required for the process of protein synthesis. tRNAs are carrying amino acids to the ribosome, where the actual protein synthesis takes place. The role of tRNA is to recognize a specific codon and to deliver the corresponding amino acid (the codon to anti-codon matching pattern)
What is a primary transcript? What is a pre-mRNA?
When eukaryotic genes of any type are transcribed, the initial product is termed a primary transcript. This RNA must undergo multistep processing before it is functional. For protein coding genes, the primary transcript is caled pre-mRNA
