Genetic Code and Transcription Flashcards
The Genetic code is what 3 features?
- Nonoverlapping: Any single ribonucleotide within mRNA is part of one triplet
- Colinear: Sequence of codons in a gene is colinear
- Nearly universal: A single coding dictionary is used by viruses,
prokaryotes, archaea, and eukaryotes
What does messenger RNA do?
- Serves as intermediate in transferring genetic information from DNA to proteins
- Genetic information is stored in DNA
- Code that translates it to protein is in RNA
Note: mRNA is the what? tRNA is what? rRNA is what?
- mRNA: codon
- tRNA: anticodon
-rRNA: site
The 3rd base pairing is known as the what?
WOBBLE!!!
Reminder, first two must sit more stably, so the 3rd one is the wobbly one in accordance with the Wobble Hypothesis
The 3rd base which is the wobble one is which type of RNA?
mRNA
Explain the initiator codon
- Methionine (AUG)
- Initial amino acid incorporated into ALL proteins
- In bacteria: modified form of methionine
Explain the Termination codons
- UAG, UAA, UGA
- Do NOT code for any amino acid
- Are not recognized by tRNA
- Translation terminated when these codons are encountered
Define Missense Mutations
- Mutations that change the amino acid in the gene
- Ex.) Change from Serine –> Phenylalanine
Define Nonsense mutations
- Mutations that produce a stop codon internally in gene
- Translation is terminated
- Partial polypeptide is produced
- Ex.) Serine –> STOP codon
Define Frameshift mutations
Additions or deletions of bases leading to change in the read out
Explain mItochondrial DNA
- Revealed exceptions to universal genetic code
- Codon UGA normally specifies termination
- mtDNA UGA codon encodes tryptophan in yeast and humans - Codon AUA normally specifies isoleucine
- Human mitochondria encodes internal insertion of
methionine
Explain Overlapping genes
- Single mRNA has multiple initiation points
- Creates different reading frames
- Specifies more than one polypeptide
Define ORF: Open Reading Frame
- DNA sequence produces RNA with start and stop
- Series of triplet codons specify amino acids to make polypeptide
Explain Transcription
- RNA synthesized on DNA template
- Genetic information stored in DNA is transferred to RNA
- Serves as intermediate molecule between DNA and proteins
- Each triplet codon is complementary to anticodon of tRNA
Explain RNA Polymerase
- Enzyme directs synthesis of RNA using DNA template
- Nucleotides contain ribose, not deoxyribose
- No primer required for initiation
- They can start from scratch aka DE NOVO!!!
Define Promoters
- Transcription results in ssRNA
- Template strand is transcribed
- Transcription begins with template binding by RNA polymerase at promoter
- Promoters: Specific DNA sequences in 5′ region upstream of initial transcription point
- σ subunit responsible for promoter recognition (initiation of transcription)
T/F: Promoters are always upstream to the + site
TRUE!!
Pol 2 makes what type of RNA?
mRNA
What happens during the Transcription start site
- DNA double helix is denatured: unwound to make template strand accessible for RNA polymerase
- Interaction of promoters and RNA polymerase regulates efficiency of transcription
What are Consensus sequences?
DNA sequences homologous in different genes of same organism
What are the 2 consensus sequences of E. coli promoters?
- TTGACA and TATAAT (Pribnow box)
- Positioned at −35 and −10 with respect to the transcription initiation site
- (-10) = 10 bases before the start site
Explain Chain Elongation
- Ribosomes are added to RNA chain
- σ subunit dissociates from holoenzyme
- Elongation proceeds under direction of core enzyme
In bacteria, there are 2 type of Terminations involving rho. Explain them
Rho-dependent: rho protein binds to RNA sequences and uses ATP hydrolysis to “catch up” with RNA polymerases terminating the transcription
Rho-Independent: “intrinsic termination” meaning signal sequence is on the RNA once it is made.
Explain Termination
- Enzyme traverses entire gene
until a termination nucleotide
sequence is encountered - In bacteria: Termination
transcribed into RNA causes
newly formed transcript to fold
back on itself (hairpin) - Rho-dependent termination
depends on the rho (ρ)
termination factor
Explain Transcription in Eukaryotes
- 3 types of RNA polymerases
- Occurs within nucleus (unlike prokaryotes)
- mRNA must leave nucleus for translation
- Chromatin remodeling: Chromatin must uncoil to make DNA accessible to RNA Pol
- RNA polymerases rely on transcription factors (TFs) to scan/bind DNA
- Enhancers and silencers control transcription regulation
- RNA Pol I,II, and III involved`
RNA Pol 1 Product AND Location
Product: rRNA
Location: Nucleolus
RNA Pol 2 Product and Location
Product: mRNA, snRNA
Location: Nucleoplasm
RNA Pol 3 Product and Location
Product: 5SrRNA and tRNA
Location: Nucleoplasm
Give me everything you know about RNA Pol 2 (long answer)
- Responsible for transcription of wide range of genes in
eukaryotes - Activity of RNAP II is dependent on cis-acting elements
and trans-acting transcription factors - RNAP II core-promoter determines where RNAP II binds
to DNA - Regulatory sequences influence efficiency of transcription initiation by RNAP II
- Proximal-promoter elements
- Enhancers
- Silencers - TATA box involved here
What is the TATA Box?
- Core-promoter element
- Binds TATA-binding protein (TBP) of transcription factor TFIID: determines start transcription start site
Explain Enhancers and Silencers
- Found upstream, within, or downstream of gene
- Enhancers increase transcription levels; silencers decrease them
- Modulate transcription from a distance
- Act to increase or decrease transcription in response to cell’s requirement for gene product
Explain Transcription Factors and provide 2 examples
- Transcription factors facilitate RNAP II binding and initiation of transcription
EXAMPLES:
- General transcription factors: Required for all RN
AP II-mediated transcription
- Transcription activators and repressors: Influence efficiency or rate of RNAP II transcription
initiation
Cap and Tail
- Eukaryotic mRNAs require processing to produce mature m
RNAs - Posttranscriptional modifications
* Addition of 5′ cap (7-mG cap)
* Addition of 3′ tail (poly-A tail)
* Excision of introns
Explain Introns (intervening sequences)
- Regions of initial RNA transcript not expressed in amino acid sequence of protein
- DNA sequences not represented in final mRNA product
- Exons are sequence retained and expressed
- Prokaryotes do not have introns
- Heteroduplexes: Introns present in DNA but not mRNA loop out
Understand Posttranscriptional modifications: Splicing
- Introns are removed by splicing
- Exons are then joined together in mature mRNA
- Mature mRNA is smaller than initial RNA
Why do we even have introns?
Introns give diversity depending on how splicing takes place
Ex.) Hemoglobin and Myoglobin
Define Self-Splicing RNAs
Self-excision group I introns
occurs in bacteria, lower
eukaryotes, and higher
plants
What is Spliceosome and what does the Reaction involve?
- Pre-mRNA introns spliced
out by spliceosome - Reaction involves:
* Formation of lariat structure
* Splice donor and acceptor sites
* Branch point sequence
What are the 2 forms of RNA editing?
Substitution editing and Insertion/deletion editing
Define Substitution editing
Identities of individual nucleotide bases are altered; prevalent in mitochondria and chloroplast RNA derived in plants
Define Insertion/Deletion editing
- Nucleotides are added/deleted from total number of bases
- Prevalent in mitochondrial and chloroplast RNAs
What does it mean that the genetic code is DEGENERATE?
- Many amino acids are specified by more than one codon
- Ex.) UCU, UCC, UCA, and UCG all code for Serine
What are the only 2 amino acids encoded by a SINGLE codon?
Tryptophan and Methionine
