Chapter 7: RNA And The Genetic Code Flashcards
Coding strand
DNA coding strand is identical to the mRNA (except T for U)
Template strand
DNA template strand is complementary and antiparallel to the mRNA
What is the most abundant type of RNA?
MRNA, followed by tRNA
What is the structure of tRNA?
Folded strand of RNA that includes a three nucleotide anticodon that recognizes and pairs with the appropriate codon on an mRNA molecule while in the ribosome
Charged or activated tRNA
When amino acids are connected to the 3’ end of a tRNA molecule
Aminoacyl-tRNA synthetase
Each type of amino acid is activated by a different aminoacyl-tRNA synthetase that requires two high-energy bonds from ATP, implying that the attachment of the amino acid is an energy-rich bond; each tRNA has a CCA nucleotide sequence where the amino acid binds; the high-energy aminoacyl-tRNA bond will be used to supply the nergy needed to crate a peptide bond during translation
What are the functions of rRNA?
Helps catalyze the formation of peptide bonds and is important in splicing out its own introns within the nucleus
Wobble position
Variable third base in the codon; evolutionary development designed to protect against mutations in the coding regions of our RNA; these mutations tend to be silent or degenerate
What enzymes are involved in transcription?
Helicase and topoisomerase are involved in unwinding the dsDNA and preventing the formation of supercoils (like in replication)
RNA polymerase II is the main player in transcribing mRNA and it binding site in the promoter is known as the TATA box
Transcription factors
Help the RNA polymerase locate and bind to this promotor region of the DNA, helping to establish where transcription will start
Unlike DNA polymerase III, RNA polymerase does not require an RNA primer to start generating a transcript
RNA polymerase I
Located in the nucleolus and synthesizes rRNA
RNA polymerase II
Located in the nucleus and synthesizes hnRNA (pre-processed mRNA) and some small nuclear RNA (snRNA)
RNA polymerase III
Located in the nucleus and synthesizes tRNA and some rRNA
Spliceosomes
Small nuclear RNA (snRNA) molecules couple with proteins known as small nuclear ribonucleoproteins (snRNPs); the snRNA/snRNP complex recognizes both the 5’ and 3’ splice sites of the introns; these noncoding sequences are excised in the form of a lariat and then degraded
5’ Cap
7-methylguanylate triphosphate cap; actually added during the process of transcription and is recognized by the ribosome as the binding site; protects the mRNA from degradation in the cytoplasm
3’ Poly-A-Tail
Added to the 3’ end of the mRNA transcript and protects the message against rapid degradation; it is composed of adenine bases; the longer the poly-a tail, the more time the mRNA will be able to survive before being digested in the cytoplasm; also assists with the export of mature mRNA from the nucleus
Alternative splicing
The primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene
TATA box
Part of the promotor to which RNA polymerase binds; located at -25
What are the three binding sites in the ribosome for tRNA?
A site (aminoacyl), P site (peptidyl) and the E site (exit)
What are the four strands of rRNA in eukaryotic ribosomes?
28S, 18S, 5.8S, and the 5S rRNAs; the “S” values indicate the size of the strand
What rRNA strands does RNA polymerase I synthesize?
28S, 18S, and 5.8S rRNAs; results in a 45S ribosomal precursor RNA; processed to become the 18S rRNA of the 40S (small) ribosomal subunit and to the 28S and 5.8S rRNAs of the 60S (large) ribosomal subunit
What rRNA strands does RNA polymerase III synthesize?
5S rRNA which is also found in the 60S ribosomal subunit; this process takes place outside of the nucleolus
Initiation of translation
The small ribosomal subunit binds to the mRNA; in prokaryotes, the small subunit binds to the Shine-Dalgarno sequence in the 5’ UTR of the mRNA; in eukaryotes, the small subunit binds to the 5’ cap structure; the charged initiator tRNA binds to the AUG start codon through base-pairing with its anticodon within the P site of the ribosome; the large subunit then binds to the small subunit, forming the completed initiation complex which is assisted by initiation factors (IFs) that are not permanently associated with the ribosome
What is the initial amino acid in prokaryotes? Eukaryotes?
N-formylmethionine (fMet) and methionine (Met)
Elongation of translation
3-step cycle that is repeated for each amino acid added to the protein after the initiator methionine; ribosome moves in the 5’ to 3’ direction along the mRNA, synthesizing the protein from its amino (N) to carboxyl (C) terminus
A site
Holds the incoming aminoacyl-tRNA complex; this is the next amino acid that is being added to the growing chain and is determined by the mRNA codon within the A site
P site
Holds the tRNA that carries the growing polypeptide chain; also where the first amino acid (methionine) binds because it is starting the polypeptide chain; a peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site; this requires peptidyl transferase (which is part of the large subunit) and GTP (for energy)
E site
Where the now inactivated (uncharged) tRNA pauses transiently before exiting the ribosome; as the now uncharged tRNA enters the E site, it quickly unbinds with the mRNA and is ready to be recharged
Elongation factors
Assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used
Signal sequences
Designate a particular destination for the protein; for peptides that will be secreted, such as hormones and digestive enzymes, a signal sequence directs the ribosome to move to the ER; other signal sequences direct proteins to the nucleus, lysosomes, or cell membrane
Termination of translation
A protein called release factor (RF) binds to the termination codon, causing a water molecule to be added to the polypeptide chain; this allows peptidyl transferase and termination factors to hydrolyze the completed polypeptide chain from the final tRNA; the polypeptide chain will then be released from the tRNA in the P site, and the two ribosomal subunits will dissociate
Chaperones
Main function is to assist in the protein-folding process
Posttranslational processing
Modified by cleavage events (ex. Insulin, cleavage of signal sequence); proper folding (with chaperones); quaternary structure (involves combination with other subunits); addition of biomolecules (phosphorylation - addition of phosphates by protein kinases to activate or deactivate proteins; carboxylation - addition of carboxylic acid groups, usually to serve as calcium-binding sites; glycosylation - addition of oligosaccharides as proteins pass through the ER and GA to determine cellular destination; prenylation - addition of lipid groups to certain membrane-bound enzymes)
Operon
Cluster of genes transcribed as a single mRNA; common in prokaryotic cells
Jacob-Monod model
Describe the structure and function of operons
Structural gene
Codes for the protein of interest
Operator site
A nontranscribable region of DNA that is capable of binding a repressor protein
Promoter site
Provides a place for RNA polymerase to bind
Regulator gene
Codes for a protein known as the repressor
Inducible systems
Repressor is bound tightly to the operator system and thereby acts as a roadback; RNA polymerase is unable to get from the promoter to the structural gene because the repressor is in the way; to remove the block, an inducer must bind the repressor protein so that RNA polymerase can move down the gene
Catabolite activator protein (CAP)
Transcriptional activator used by E. coli when glucose levels are low to signal that alternative carbon sources should be used; falling levels of glucose cause an increase in the signaling molecule cAMP which binds to CAP; conformational change in CAP allows it to bind to the promoter region of the operon, increasing transcription of the lactase gene
Repressible system
Allow constant production of a protein product; the repressor made by the regulator gene is inactive until it binds to a corepressor; this complex then binds the operator site to prevent further transcription; tend to serve as negative feedback; referred to as negative control mechanisms
What type of operon is the trp operon?
Repressible system
What type of operon is the lac operon?
Inducible system
Transcription factors
Transcription-activating proteins that search the DNA looking for specific DNA-binding motifs; tend to have two recognizable domains: DNA-binding domain and an activation domain
DNA-binding domain
Binds to a specific nucleotide sequence in the promoter region or to a DNA response element (a sequence of DNA that binds only to specific transcription factors) to help in the recruitment of transcriptional machinery
Activation domain
Allows for binding of several transcription factors and other important regulatory proteins (such as RNA polymerase and histone acetylases which function in the remodeling of the chromatin structure)
Enhancers
Allows for control of one’s gene expression by multiple signals; can be up to 1000 bp away from the gene they regulate (sometimes DNA must form a hairpin loop);outside the normal promoter regions and can be recognized by specific transcription factors to enhance transcription levels
Upstream promoter elements
Must be within 25 bps of the start of a gene
Gene duplication
Genes can be duplicated in series on the same chromosome; alternatively, they can be duplicated in parallel by opening the gene with helicases and permitting DNA replication only of that gene
Histone acetylation
Transcription factors that bind to the DNA can recruit other coactivators such as histone acetylases - involved in chromosome remodeling because they acetylate lysine residues found in the amino terminal tail regions of histone proteins; decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA, resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA
Histone deacetylases
Proteins that function to remove acetyl groups from histones, which results in a closed chromatin conformation and overall decrease in gene expression levels in the cell
DNA methylation
DNA methylases add methyl groups to cytosine and adenine nucleotides - often linked to silencing of gene expression; heterochromatin regions are much more heavily methylated, hindering access of the transcriptional machinery to the DNA
What are signal molecules?
Steroid hormones and second messengers which bind to their receptors in the nucleus
What are transcription factors?
Receptors that use their DNA binding domain to attach to a particular sequence in DNA called the response element; once bound to the response element, these transcription factors can then promote increased expression of the relevant gene
