RNA and Genetic Code Flashcards
mRNA
Carries information from DNA by traveling from the nucleus (where is is transcribed) to the cytoplasm (where is it translated)
How is mRNA synthesized?
- 5’ to 3’
- antiparallel to complementary strand of DNA
How is the protein sythensized
- from animo to carboxy terminus
- mRNA is red 5’ to 3’
tRNA
- converts language of nucleic acids into amino acids and peptides
- anticodon
- charged tRNA when amino acids are attached to it
- tRNA is found in the cytoplasm
Aminoacyl-tRNA-synthetase
- puts the amino acid on the tRNA
- tRNA has a CCA nucleotide sequence in which the AA binds
rRNA
- synthesized in the nucleolus
- ribozymes - enzymes made from RNA molecules instead of protein
- catalytic function: creates peptide bonds between amino acids
What are the 3 stop codons?
UAA, UAG, UGA
Why is the genetic code degenerate?
-because more than one codon can specify for a single amino acid
Point mutation
-where one nucleotide replaces another nucleotide
1) Missense mutation
2) Nonsense mutation
Missence mutation
-a type of point mutation
-results in the substitution of one amino acid for another
Encoded protein: One amino acid is changed in the protein; variable effects on function depending on specific change
Nonsense mutation
-a type of point mutation
-results in a premature stop codon (truncation mutation)
Encoded protein: Early truncation; variable effect but usually more severe than missense mutation
Transcription
-creation of mRNA from DNA template
Frameshift
Insertion or deletion of bases, creating a shift in the reading frame of the mRNA
Encoded protein: Change in most amino acids after the site of insertion or deletion; usually the most severe of the mutation types
Template strand
- the DNA strand where mRNA is synthesized
- aka: antisense strand
- mRNA strand is antiparallel and complementary to the template strand
RNA polymerase
- how RNA is synthesized
- binds at the PROMOTER
What RNA polymerase transcribes in eukaryotes?
RNA polymerase II
-binds at the TATA box (promotor)
Transcription factors
-help bind the RNA polymerase bind to the promoter region of DNA
RNA polymerase I, II, III in eukaryotes
I = synthesizes rRNA II = synthesizes the mRNA III = synthesizes tRNA and some rRNA
How does RNA polymerase read?
-reads 3’ to 5’ - so builds the mRNA 5’ to 3’
Coding strand
- sense strand of the DNA
- not used in template during transcription
- coding strand is identical to the mRNA transcript - but thymines replaced by uracils
Posttranscriptional modifications
1) Addition of guanine 5’cap
2) Addition of poly 3’ A tail
3) Intron / exon splicing
Splicing
-Removal of introns (non-coding regions) and joining of exons (coding sequences). Uses snRNA and snRNPs in the spliceosome to crease lariat, which is degraded. Exons are ligated together.
Spliceosome
-snRNA with snRNPs
Alternative splicing
- primary transcript of pre-mRNA may be spliced togther in different ways to produce multiple variants of proteins encoded by the same oriignal gene
- basically, produces different proteins from the same gene
5’cap
Addition of a 7-methylguanylate triphosphate cap to the 5 end of the transcrip
poly 3’ A tail
Addition of adenosine bases to the 3 end to protect against degradation
Heterogeneous nuclear RNA (hnRNA)
Primary transcript; mRNA derived from hnRNA via posttranslational modification
-before mRNA; in nucleus
Initiation
Prokaryotes:
What is the main function of the ribosome?
to combine the mRNA and the charged aminoacyl-tRNA complex to generate the protein
What are the 4 strands of rRNA found in the eukaryotic ribosome?
28S, 18S, 5.8S, 5S
The two subunits that make up the whole 80s ribosome are the —- subunit which contains the —–, —-, and — rRNA strand and the — subunit which contains the —- rRNA strand.
60S, 28S, 5.8S, 5S, 40S, 18S
The 70S ribosome found in a prokaryote is composed of a —– subunit that contains a —- and —– rRNA strand and the —– subunit contains a —- rRNA strand.
50S, 5S, 23S, 30S, 16S
What occurs during the initiation phase of translation in prokaryotes?
the 30S ribosomal subunit attaches to the Shine-Dalgarno sequence and scans for a start codon; it also lays down N-formylmethionine in the P site of the ribosome
What occurs during the initiation of translation in eukaryotes?
the 40S ribosome attaches to the 5’ cap and scans for a start codon; it lays down methionine in the P site of the ribosome
A site
Binds incoming aminoacyl-tRNA- anticodon pairing
P site
holds growing polypeptide until peptidyl transferase forms peptide bond and polypeptide is handed to A site
E site
Transiently holds uncharged tRNA as it is ready to leave
The peptide bonds formed during translation are formed using —- and ——.
peptidyl transferase and GTP
What triggers the start of the termination stage of translation? What happens after that?
the codon in the A site is a stop codon;a release factor places a water molecule on the polypeptide chain and thus releases the protein by hydrolysis
What are the 4 post-translational modifications made?
folding by chaperons, formation of quaternary structures, cleavage of proteins or signal sequences, and the covalent addition of other biomolecules
carboxylation
is the addition of carboxylic acid groups, usually to serve as calcium binding sites.
glycosylation
the addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination.
prenylation
is the addition of lipid groups to certain membrane bound enzymes.
Phosphorylation
Addition of phosphates by protein kinases to activate or deactivate proteins
Jacob-Monod Model
- describes the structure and function of operons
- operons contain structural genes, an operator site, a promoter site, a regulatory gene
Structural genes
-code for protein of interest
Operator site
-where repressor protein can bind
Promotor site
-where RNA polymerase binds
Regulator gene
Transcribed to form repressor protein
Operons
Include both inducible and repressible systems, and offer a simple on-off switch for gene control
Positive control system
require the binding of a protein to the operator site to increase transcription
Negative control system
Require the binding of a protein to the operator site to decrease transcription
Inducible systems
- repressor is binded tightly to the operator, prevents RNA polymerase from binding to transcribe - negative control
- to remove, an inducer binds to repressor to unblock operator site, so RNA polymerase can bind
Lac operon
- example of a inducible system
- only want to use this option of lactose is high and glucose is low
- inducer: lactose
- assisted by the binding of CAP - low glucose, high levels of cAMP, cAMP binds to CAP
- CAP binds to promoter, increases the transcription of the lactase gene - positive control
Repressible system
- allow constant protein production
- repressor is inactive until it binds to a corepressor
- complex then binds to operator site to prevent transcription
-negative feedback - final product can be used as a corepressor
Trp operon
- repressible system
- when Trp is high in the environment, acts as a corepressor
The DNA regulatory base sequences ( promoters, enhancers, and response elements) are known as —— because they are in the same vicinity as the gene they control.
cis regulators
2 binding domains of transcription factors
1) DNA binding domain - binds to specific nucleotide sequences in the promoter region to help recruit transcription machinery
2) Activation domain - allows for binding of several TFs and other important regulatory proteins
Enhancers
- amplify gene transcription
- enhancer binds to promotor regions to enhance transcription
Gene duplication
- duplicating the relevant gene
- genes can be duplicated in series on the same chromosome
Heterochromatin
- tightly coiled DNA that appears DARK under microscope
- inactive - tight coiling makes it unavailable to transcription factors
- greater methylation
Euchromatin
- tightly coiled DNA that appears DARK under microscope
- inactive - tight coiling makes it unavailable to transcription factors
Histone Acetylation
- histone acetylases - acetylate lysine residues
- acetylation of histone proteins decreases the positive charge on the lysine residues and weakens the interaction of the histone with DNA
- thus - acetylation loosens the DNA and allows for easier transcription
Histone Deacteylation
-removes acetyl groups from lysine - strengthens interaction of DNA and histone - will decrease gene expression levels - closed conformation
DNA methylation
-adds methyl groups to Cytosine and Adenine- silences gene expression
In an enhancer, what are the difference between signal molecules, transcription factors and response elements
Single molecules include steroid hormones and second messengers, which bind to their receptors in the nucleus. These receptors are transcription factors that use their DNA- binding domain attach to a particular sequence in DNA called a response element. Once bonded to the response element, these transcription factors can then promote increased expression of relevant gene.
By what histone and DNA modification can genes be silenced in eukaryotic cells? Would these processes increase the proportion of hetrochromatin or euchromotin?
Histone deacetylation and DNA methylation will both down regulate the transcription of Gene. These processes allow the relevant DNA to be clumped more tightly and increase heterochromatin.
peptidyl transferase role
It catalyzes the formation of a peptide bond
It connects the incoming amino terminal to the previous carboxyl terminal. so its a amide linkage
How are enhancers recognized?
By specific transcription factors
specific transcription factors
bind to specific DNA sequences, such as an enhancer and to RNA polymerase at a single promotor sequence.
