RNA is the initial product of all genes. It differs from DNA in that it uses the...
5 carbon sugar ribose in its nucleotides and doesn't use Thymine but instead uses Uracil (U).
RNA molecules may be functional and categorized as:
Transfer RNA (tRNA)- molecules that transport amino acids to ribosomes where they are used during the translation of mRNA into a polypeptide.
Ribosomal RNA (rRNA)- form components of the ribosomes.
Small nuclear RNAs (snRNAs)- small RNA molecules which remain in the nucleus of eukaryotes and function in splicing RNA. They combine with small nuclear proteins and form snRNPswhen involved in splicing.
Small cytoplasmic RNAs (scRNAs)- Combine with polypeptides that are destined for secretion, when they are being synthesized, so that they will enter the lumen of the endoplasmic reticulum.
Functioning of both RNA and DNA is dependent on:
Complementary base pairing between RNA and DNA strands
Pairing between proteins and specific single or double stranded nucleic acid regions.
RNA molecules may be informational in that their nucleotide sequence and translated into an amino acid sequence thereby forming a polypeptide. Such informational RNA molecules are referred to as...
messenger RNA (mRNA)
True or False: For any individual gene only one of the DNA strands serves as the template, the other is referred to as the nontemplate.
True or False: The template is always read in a 3' to 5' orientation by enzymes when synthesizing nucleic acids
The enzyme that transcribes the DNA into RNA is called RNA polymerase. There is only one RNA polymerase in prokaryotes but 3 in eukaryotes. What are the 3 RNA polymerase in Eukaryotes and what do they do?
RNA polymerase I transcribes rRN
RNA polymerase II transcribes mRNA
RNA polymerase III transcribes tRNA
RNA is always transcribed (synthesized) in a _____ direction.
5' to 3'
What is Initiation?
RNA polymerase attaches to the promoter region that is upstream (on the 5' side of the nontemplate) from the DNA to be transcribed. This identifies which strand is to be the template. There are sequences of DNA that are found associated with this initiation of transcription, usually at -10 and -35 base positions upstream from where transcription begins in prokaryotes
What is Elongation?
Ribonucleoside triphosphates are added to the growing RNA strand by cleaving their terminal diphosphates and attaching the nucleotides 5' end to the 3' end of the RNA strand. The energy for this is provided by the removal of the phosphates.
What is Termination?
In prokaryotes the termination of transcription may be signaled by a protein (rho) that attaches to the growing RNA and follows the RNA polymerase in a 5'to3' direction. When the RNA polymerase stalls at a GC rich region of DNA the rho catches up with the polymerase leading to termination. Alternatively termination may be signaled in both prokaryotes and eukaryotes, by a sequence of approximately 40bp. This sequence has a stretch of GCs followed by 6 or more A's on the template. The GC region codes for RNA that forms a hairpin that is recognized by the RNA polymerase as a termination signal. The A's pair with complementary U's on the RNA weakly because they only have two hydrogen bonds per pair, therefore represent an easy region where the RNA and DNA may be separated
Following transcription the eukaryotic RNA is processed prior to leaving the nucleus. The processing of pre-mRNA is:
First a 7-methylguanosine cap is attached to the 5' end of the transcript via a triphosphate bond.
Second, a AAUAAA sequence on the RNA is recognized and the RNA is cleaved 20 nucleotides downstream.
Third, a 150-200 base long poly-A tail is attached to the 3' end.
Fourth introns are removed and exons spliced together. Fig.3-11.
The result is the mRNA molecule. In Eukaryotes there is one polypeptide message on a single mRNA (monocistronic), but prokaryotes have messages for more than one polypeptide (polycistronic).
What is a spliceosome?
a set of snRNPs which together form a structure
What are ribozymes?
RNAs are capable of catalyzing their own splicing.
What are the different types of PROTEIN STRUCTURE?
Primary structure- sequence of amino acids
Secondary structure- repetitive structure due to hydrogen bonds forming between regions of the carbon-nitrogen backbone of the polypeptide. Forms alpha helix, etc.
Tertiary structure- Three dimensional structure formed by bonding between side chains.
Quaternary structure- Emergent structure resulting from more than one polypeptide binding together.
Remember that amino acids all have an amino and carboxyl group.
Proteins may be globular (e.g. enzymes or antibodies) or fibrous (structural).
The three dimensional shape of the polypeptide is important because it generates the____.
active site (i.e., the region where the enzyme binds with the substrates).
A sequence of three nucleotides in a loop of a tRNA molecule (the _____) will hydrogen bond with 3 complementary nucleotides of a _____.
Amino acids are bound to tRNAs with the assistance of enzymes ______.
aminoacyl tRNA synthetases
Initiation of translation differs a bit between prokaryotes and eukaryotes. In prokaryotes:
A sequence at the 5' end of the mRNA that will not be translated (the Shine-Dalgarno sequence) pairs with the 3' end of the small ribosomal subunits 16S rRNA. This positions the mRNA relative to the ribosome such that an initiation codon for N-formylmethionine is positioned in the P site. Between the Shine-Dalgarno sequence and the initiation codon is a variable amount of leader sequence DNA that is not translated.
Initiation of translation differs a bit between prokaryotes and eukaryotes. In Eukaryotes:
The 7-methylguanosine cap plays the role of the Shine-Dalgarno sequence and the first codon to be translated is for methionine. After the codon is situated in the P-site and an appropriate charged tRNA arrives together with initiation factor1,2,and 3 proteins the large ribosomal subunit joins with the small subunit.
Elongation (in translation) of the polypeptide involves new charged tRNAs arriving at the____ and attaching their amino acids amino group to the carboxyl group of the amino acid charging the tRNA in the ____ by a peptide bond
A-site , P-site
The energy for the reaction involving the A-site and P-site, comes from _____.
_____also provides the energy for the translocation of the ribosome 3 nucleotides down the mRNA.
Elongation and translocation continue until a stop signal arrives in the _____.
The sequence of codons in RNA and the sequence of amino acids in proteins are_____.
The DNA template that contains the sequence of nucleotides that code for the most common form of the polypeptide being studied in a natural population of individuals is referred to as the______ allele.
Transcripts that are missing (or have an additional) nucleotide generally have the message incorrect for all codons downstream from the nucleotide of interest. They lead to______.
Mutant alleles may produce no functional polypeptide, in which case they are called ______.
Some nucleotide substitutions cause no change in the polypeptide (because of the redundancy of the genetic code) they are called_______.
Diploid individuals who possess one wild type allele (that codes for a nonfunctional protein and is therefore called a loss of function mutation) and one mutant allele may have sufficient protein to be functionally normal. This is referred to as ________ and the wild type allele would be considered ______.
If the amount of protein produced by an individual with only one wild type allele was insufficient for it to be functionally normal, the wild type allele would be ______. This would be an example of ______.