Chapter 7 - RNA and the Genetic Code Flashcards
Gene
a unit of DNA that encodes a specific protein or RNA molecule, and thru transcription and translation, that gene can be expressed
Messenger RNA (mRNA)
carries the info specifying the amino acid sequence of the protein to the ribosome; mRNA is transcribed from template DNA strands by RNA polymerase enzymes in the nucleus of cells
Which type of RNA is the only one that contains information that is translated into proteins?
Messenger RNA
In eukaryotes, mRNA is monocistronic. What does this mean?
each mRNA molecule translates into only one protein product
Can mRNA ever be polycistronic?
Yes, mRNA may be polycistronic in prokaryotes
Can mRNA undergo posttranscriptional modifications?
Yes, prior to its release from the nucleus
Transfer RNA (tRNA)
converts the language of nucleic acids to the language of AAs and peptides; each tRNA molecule contains a folded strand of RNA that includes a 3-nucleotide anticodon
What does an anticodon do?
it recognizes and pairs with the appropriate codon on an mRNA molecules within the ribosome
What is a charged or activated tRNA molecule?
One that is connected with an AA, mature tRNA is found in the cytoplasm
aminoacyl-tRNA synthetase
different types of this enzyme activate each type of amino acid and requires two high-energy bonds from ATP; this implies the attachment of the AA is an energy-rich bond
How is energy supplied to create a peptide bond during translation?
the high-energy aminoacyl-tRNA bond will be used to supply the energy
Ribosomal RNA (rRNA)
synthesized in nucleolus; integral part of ribosomal machinery used during protein assembly in the cytoplasm
Why do many rRNA molecules function as ribozymes? (Enzymes made of RNA molecules instead of peptides)
rRNA helps catalyze the formation of peptide bonds and is also important in splicing out its own introns within the nucleus
What are the stop codons?
UAG, UAA, UGA. (Ur A Gay) (Ur An Ass) (U Gay Ass)
What is the start codon?
AUG (Met)
Why is the genetic code degenerate?
More than one codon can specify a single amino acid. All except Met and Trp are encoded by multiple codons
What is the wobble position of a codon?
for AAs with multiple codons, the first two bases are usually the same, and the third base is variable; this variable third base is the wobble position
What mutations in the wobble position are most common?
Silent or degenerate mutations; there is no effect on the expression of the AA and no adverse effects on the polypeptide sequence
Point Mutation
a mutation that affects only one of the nucleotides in a codon
What are the types of point mutations?
missense and nonsense mutations
What are expressed mutations?
they are point mutations that can affect the primary amino acid sequence of the protein
Missense Mutation
a mutation where one amino acid substitutes for another
Nonsense Mutation
a mutation where the codon now encodes for a premature stop codon (aka truncation mutation)
Frameshift Mutation
occurs when some number of nucleotides are added or deleted from the mRNA sequence; the effects are typically more severe than point mutations
Transcription
creation of mRNA from a DNA template
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 nucleus, synthesizes tRNA and some rRNA
Coding Strand (Sense Strand) of DNA
is not used as a template during transcription; coding strand is complementary to template strand, so it’s identical to the mRNA transcript except all thymine is now uracil
heterogeneous nuclear RNA (hnRNA)
is the primary transcript formed after the DNA double helix reforms after the termination of transcription by a stop codon; mRNA is derived from hnRNA via posttranscriptional modifications
Introns
non-coding sequences within an hnRNA transcript; they are spliced out by spliceosomes
Exons
coding sequences which are ligated together during maturation of hnRNA
Why do snRNA molecules couple with small nuclear ribonucleoproteins (snRNPs) in the spliceosome?
the snRNP/snRNA complex recognizes both the 5’ and 3’ splice sites of the introns
5’ Cap
7-methylguanylate triphosphate cap added to hnRNA; added during transcription, is recognized by ribosome as binding site; protects mRNA from degradation in cytoplasm
3’ Poly-A Tail
polyadenosyl tail, protects against rapid degradation; longer the poly-A tail, the more time mRNA will be able to survive before being digested in cytoplasm; assists with export of mature mRNA from nucleus
Alternative Splicing
primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by same original gene
Nuclear Pores
allow mRNA transcripts to exit the nucleus after it is created and processed
How does translation begin?
an mRNA will find a ribosome to begin translation once in the cytoplasm
What are the three steps of translation?
initiation, elongation, and termination
Initiation
small ribosomal subunit binds mRNA; charged initiator tRNA binds to AUG start codon through base-pairing with its anticodon within the P site of ribosome
Shine-Dalgarno sequence
in prokaryotes, small subunit of ribosome binds here in the 5’ untranslated region of mRNA
What is the order of sites in the ribosome during translation?
A P E
Elongation
three-step cycle that is repeated for each AA added to protein after initiator methionine; ribosome moves in 5’ to 3’ direction along mRNA, synthesizing protein from its amino (N-) to carboxyl (C-) terminus
A site
holds incoming aminoacyl-tRNA complex, which is the next AA being added to the growing chain; determined by the mRNA codon within the A site
P site
holds tRNA that carries growing polypeptide chain; also where first AA (Met) binds. A peptide bond is formed as polypeptide is passed from tRNA in the P site to tRNA in A site (requiring peptidyl transferase) GTP is used
E site
where the now inactivated (uncharged) tRNA pauses before exiting the ribosome; quickly unbinds from mRNA as uncharged tRNA enters E site for recharging
Elongation Factors (EF)
assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once energy is used
Termination
when any of the 3 stop codons moves into the A site, a protein called release factor (RF) binds to termination codon, causing H2O to be added to polypeptide chain; H2O allows peptidyl transferase and termination factors to hydrolyze the completed polypeptide chain from final tRNA to be released
Chaperones
special class of proteins that assist in protein-folding process
Phosphorylation
addition of a phosphate group (PO4^2-) by protein kinases to activate or deactivate proteins; phosphorylation in eukaryotes is most commonly seen with serine, threonine, and tyrosine
Carboxylation
addition of COOH groups, serves as calcium-binding sites
Glycosylation
adds oligosaccharides as proteins pass thru the ER and Golgi apparatus to determine cellular destination
Prenylation
addition of lipid groups to certain membrane-bound enzymes
Operon
a cluster of genes transcribed as a single mRNA; in E. coli it is known as the trp operon (common in prokaryotic cells)
Jacob-Monod Model
used to describe structure and function of operons: operons contain structural genes, an operator site, a promoter site, and a regulator gene
Structural Gene
codes for protein of interest
Operator Site
a nontranscribable region of DNA that is capable of binding a repressor protein (upstream of structural gene)
Promoter Site
provides a place for RNA polymerase to bind (upstream of operator site)
Regulator Gene
codes for a protein known as the repressor (upstream of promoter)
What are the two types of operons?
inducible systems and repressible systems
Inducible Systems
repressor is tightly bonded to operator system and acts as a roadblock; RNA polymerase is unable to get from the promoter to the structural gene
Negative Control mechanisms
mechanisms in which binding of a protein reduces transcriptional activity
lac operon
induced by presence of lactose and is assisted by binding of catabolite activator protein (CAP)
Catabolite Activator Protein (CAP)
transcriptional activator used by E. coli when glucose levels are low to signal that alternative carbon sources should be used
Positive Control
binding of a molecules increases transcription of a gene
Repressible Systems
allow constant production of a protein product
Corepressor
activates the repressor made by the regulator gene (repressor is inactive otherwise)
trp operon
negative repressible system; when tryptophan is high in the local environment, it acts as a corepressor
Transcription Factors
transcription-activating proteins that search the DNA looking for specific DNA-binding motifs; tend to have two recognizable domains: a 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 to help in recruitment of transcriptional machinery
Activation Domain
allows for the binding of several transcription factors and other important regulatory proteins, such as RNA polymerase and histone acetylases, which function in remodeling of chromatin sturcture
Enhancers
allows for control of one gene’s expression by multiple signals
What are some common signal molecules?
cyclic AMP (cAMP), cortisol, estrogen
What are types of cis regulatory elements?
promoters, enhancers, and response elements; they’re in the same vicinity as the gene they control
What are trans regulators?
transcriptions factors that are produced and translocated back to the nucleus; they travel thru the cell to their point of actions (hence, trans)
Heterochromatin
tightly coiled DNA that appears dark under microscope; its tight coiling makes it inaccessible to the transcription machinery (these genes are inactive)
Euchromatin
looser and appears light under microscope; transcription machinery can access the genes of interest, so these genes are active
Histone Acetylation
histone acetylases are involved in chromatin remodeling, they acetylate lysine residues found in the amino terminal tail regions of histone proteins
Acetylation
decreases histone’s 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 transcriptional machinery to DNA
Histone deacetylases
proteins that remove acetyl groups from histones, resulting in a closed chromatin conformation and overall decrease in gene expression levels
DNA Methylation
chromatin remodeling and regulation of gene expression
DNA Methylases
add methyl groups to cytosine and adenine nucleotides; often results in silencing of gene expression
Why are heterochromatin regions of DNA much more heavily methylated or in other words, have much more hindered access to transcriptional machinery?
heterochromatin genes are inactive
