Ch 7 RNA and The Genetic Code - and control of gene expression in prokaryotes Flashcards
Central dogma of molecular biology
DNA replicates back into DNA. DNA is transcribed into RNA. RNA is reverse transcribed back into DNA. RNA is translated into proteins
Gene
Previous definition- a unit of DNA that encodes a specific protein or RNA molecule and through transcription and translation the gene can be expressed
Messenger RNA (mRNA)
Carries info specifying the amino acid sequence of the protein to the ribosome.
Transcribed from template dna strands by RNA polymerase enzymes in the nucleus of the cell.
Only type of RNA that contains info that is translated into protein
Codons
Genetic code tables. Messenger RNA is read in three nucleotide sequence called codons in order to produce proteins.
Translated into an amino acid.
Code for one amino acid each - there are 64.
Monocistronic
In eukaryotes this defines mRNA, which means that each mRNA molecule translates into only one protein
Polycistronic
Prokaryotic cells - starting process of translation at different locations in the mRNA can result in different proteins
Transfer RNA (tRNA)
Responsible for converting the language of nucleic acids to the language of amino acids and peptides.
Each tRNA contains a folded strand of RNA that includes a three-nucleotide anticodon which recognizes and pairs with the appropriate codon in an mRNA while in the ribosome.
Mature tRNA is found in the cytoplasm
Charged or activated tRNA molecules
To become part of a nascent polypeptide in the ribosome, amino acids are connected to a specific tRNA molecule which are said to be charged or activated
Aminoacyl-tRNA synthetase
Each amino acid is activated by a different one of these.
Each requires two high energy bonds from ATP.
Transfers the activated amino acid to the 3’ end of the correct tRNA.
Each tRNA has a CCA nucleotide sequence where the amino acid binds
Ribosomal RNA (rRNA)
Synthesized in the nucleus; functions as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm.
Helps catalyze formation of peptide bonds and is important in splicing out its own introns within the nucleus
Ribozymes
Many rRNA molecules function as this; they are enzymes made of RNA molecules instead of peptides
Start codon
Methionine. All proteins begin with this.
AUG
Stop codons
UAG, UGA, UAA
Anticodons
Allows tRNA to pair with mRNA.
Will be antiparallel
Degenerate
Generic code is this because more than one codon can specify a single amino acid. All amino acids except for methionine and tryptophan are coded by multiple codons
Wobble position
Third position in a codon.
It is variable and the variability is meant to protect against mutations in coding regions. Codons only require first two nucleotides be correct.
Mutations often called silent or degenerate
Point mutation
Mutation affected one of the nucleotides in the codon.
In the third position it is still silent.
Expressed mutations
Point mutations that can affect primary amino acid sequence of the protein
Two categories: missense and nonsense
Missense mutation
A type of expressed point mutation where one amino acid substitutes for another
Nonsense mutation
An expressed point mutation where the codon now encodes for a premature stop codon.
Also called truncation mutation
Reading frame
The three nucleotides of a codon
Frameshift mutation
Occurs when some number of nucleotides are added or deleted from the mRNA sequence.
Usually very severe ill effect
Transcription
The creation of mRNA from a DNA template.
RNA must be used to generate proteins because DNA cannot exist outside of the nucleus
Template strand
Also called the antisense strand.
One of the two dna strands from which mRNA is transcribed
Promoters
Specialized DNA regions which RNA polymerase uses to search for proteins
RNA polymerase II
Main player in transcribing mRNA.
Located in the nucleus; synthesizes hnRNA (preprocessed mRNA) and some small nuclear RNA (snRNA)
TATA box
RNA polymerase II’s binding site in the promoter region.
Named for high concentration of thymine and adenine bases.
Usually falls around base -25
Transcription factors
Help RNA polymerase locate and bind to the promoter region of DNA, helping to establish where transcription will start
RNA polymerase I
Located in nucleus and synthesizes rRNA
RNA polymerase III
Located in nucleus and synthesizes tRNA and some rRNA
Coding strand
Also called sense strand.
Not used as a template for transcription.
Identical to mRNA transcript except T is replaced with U
Base numbering
First base transcribed is numbered +1. To the left are negative and to the right are positive.
Heterogeneous nuclear RNA (hnRNA)
Primary transcript formed after DNA hits termination sequence or stop signal.
mRNA is derived from this via posttranscriptional modifications
Introns
Noncoding sequences.
Stay in the nucleus
Exons
Ligate coding sequences.
Exit the nucleus as part of the mRNA
Spliceosome
Accomplishes splicing which causes the maturation of hnRNA.
Splicing removes introns and exons.
Small nuclear RNA (snRNA) molecules couple with proteins known as small nuclear ribonucleoproteins (snRNPs) which recognize the 5’ to 3’ splice site of the introns
Lariat
In splicing, the noncoding sequences are excised in this form.
A lasso shaped structure.
7-methylguanylate triphosphate cap
Cap at the 5’ end of the hnRNA added during the process of transcription and recognized by the ribosome as the binding site.
Protects mRNA from degradation in the cytoplasm
Polyadenosyl (poly A) tail
Added to the 3’ end of the mRNA transcript and protects the message against rapid degradation.
Composed of adenine bases.
The longer the poly-A tail the longer the mRNA has before being digested by the cytoplasm
Alternative splicing
In eukaryotic cells, the production of multiple different but related mRNA molecules from a single primary transcript of hnRNA.
Nuclear pores
mRNA exits the nucleus through these once the transcript is created and processed
Translation
Converting mRNA transcript into a functional protein.
Requires mRNA, tRNA, ribosomes, amino acids, and energy in the form of GTP
Ribosome
Composed of proteins and rRNA.
Prokaryotes and eukaryotes both have small and large subunits that bind during protein synthesis.
Functions to bring mRNA message together with the charged aminoacyl-tRNA complex to generate protein
strands of rRNA in eukaryotes
And subunits
28S, 18S, 5.8S, 5S
S value indicates the size of the strand
5S, 5.8S, and 28S RNAs combine to form 60S large subunit. 18S RNA becomes 40S small subunit and 60S and 40S combine to form 80S ribosome
Prokaryotic subunits and strands
5S RNA and 23S RNA combine to form 50S large subunit. 16S RNA becomes 30S subunit.
30S and 50S subunits combine to form 70S ribosome
Initiation
Small ribosomal subunits bind to the mRNA
Prokaryotes - subunit binds to Shine-Dalgarno sequence in 5’ untranslated region of mRNA.
Eukaryotes- small subunit binds to 5’ cap.
Then the charged initiator tRNA binds to the start codon through base pairing with its anticodon in P site of ribosome.
Large subunit then binds with small forming initiation complex.
Starting amino acid in prokaryotes
N-formylmethionine (fMet)
Initiation factors (IF)
Assist large subunits to bind to small subunits completing initiation complex.
They are not permanently associated with the ribosome
Elongation
Three step cycle repeated for each amino acid added to protein after the initiator methionine. During ribosome moves in the 5’-3’ direction along the mRNA synthesizing from protein’s amino (N) to carboxyl (C) terminus
A site
binding site on ribosome during elongation. holds incoming aminoacyl-tRNA complex which is the next amino acid being added determined by mRNA codon in the A site
P site
binding site on ribosomeduring elongation. Holds tRNA that carries growing polypeptide chain. Where the first amino acid (methionine) binds bc it is the starting polypeptide chain. Peptide bond formed as polypeptide is passed from the tRNA in P site to tRNA in A site. Requires peptidyl transferase (enzyme that is part of the large subunit). GTP used for energy during formation of bond
E site
binding site on ribosome during elongation. Where inactivated (uncharged) tRNA pauses transiently before exiting ribosome. As now uncharged tRNA enters E site it quickly unbinds from mRNA and is ready to be recharged
Elongation factors (EF)
Locate and recruit aminoacyl-tRNA along with GTP while helping remove GDP once energy has been used.
Release factor (RF)
When any of the three stop codons moves into the A site this protein binds to the termination codon causing a water molecule to be added to the polypeptide chain which allows peptidyl transferase and termination factors to hydrolyze the completed polypeptide chain from the final tRNA
Chaperones
Specialized class of proteins - main function is to assist the protein folding process.
Post translational processing
Cleavage of proteins such as insulin or folding for proteins to become active
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 Golgi apparatus to determine cellular destination
Prenylation
Addition of lipid groups to certain membrane bound enzymes
Operon - prokaryotes
A cluster of genes transcribed as a single mRNA. Example is trp operon in E. coli; two types: inducible systems and repressible systems
Jacob-Monod model - prokaryotes
Used to describe the structure and function of operons. In this model operons contain structural genes, an operator site, a promoter site, and a regulator gene
Structural gene - prokaryotes
Jacob-Monod model of operon - codes for protein of interest
Operator site - prokaryotes
Jacob-Monod model of operon - upstream of structural gene - a nontranscribable region of DNA that is capable of binding a repressive protein.
Promoter site - prokaryotes
Jacob-Monod model of operon - upstream from operator site - similar in function to promoters in eukaryotes - provides place for RNA polymerase to bind
Regulator gene - prokaryotes
Jacob-Monod model of operon - furthest upstream - codes for protein known as the repressor
Inducible systems
Prokaryotes- the repressor is bonded tightly to the operator system and thereby acts as a roadblock. RNA polymerase is unable to get from the promoter to the structural gene. To remove block inducer must bind the repressor protein so that RNA polymerase can move down the gene. Allows gene products to be produced only when they’re needed. System is usually off
Negative control mechanisms
Example is inducible systems
Systems in which the binding of a protein reduces transcriptional activity
Lac operon
Example of inducible system - contains gene for lactase. Bacteria can digest this but it is more energetically taxing than using glucose so genes are only transcribed when glucose is low
Catabolite activator protein (CAP)
Binding of this Assists lac operon. 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
Positive control mechanism
Systems in which the binding of a molecule increases transcription of a gene
Repressible systems
Allow constant production of a protein product.
System is usually on. Trp operon is an example
Corepressor
In repressible systems repressor made by the regulator gene is inactive until it binds to this. This complex then binds the operator site to prevent further transcription.
