Genetic Code and Transcription Flashcards
1
Q
The Genetic code is what 3 features?
A
- 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
2
Q
What does messenger RNA do?
A
- 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
3
Q
Note: mRNA is the what? tRNA is what? rRNA is what?
A
- mRNA: codon
- tRNA: anticodon
-rRNA: site
4
Q
The 3rd base pairing is known as the what?
A
WOBBLE!!!
Reminder, first two must sit more stably, so the 3rd one is the wobbly one in accordance with the Wobble Hypothesis
5
Q
The 3rd base which is the wobble one is which type of RNA?
A
mRNA
6
Q
Explain the initiator codon
A
- Methionine (AUG)
- Initial amino acid incorporated into ALL proteins
- In bacteria: modified form of methionine
7
Q
Explain the Termination codons
A
- UAG, UAA, UGA
- Do NOT code for any amino acid
- Are not recognized by tRNA
- Translation terminated when these codons are encountered
8
Q
Define Missense Mutations
A
- Mutations that change the amino acid in the gene
- Ex.) Change from Serine –> Phenylalanine
9
Q
Define Nonsense mutations
A
- Mutations that produce a stop codon internally in gene
- Translation is terminated
- Partial polypeptide is produced
- Ex.) Serine –> STOP codon
10
Q
Define Frameshift mutations
A
Additions or deletions of bases leading to change in the read out
11
Q
Explain mItochondrial DNA
A
- 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
12
Q
Explain Overlapping genes
A
- Single mRNA has multiple initiation points
- Creates different reading frames
- Specifies more than one polypeptide
13
Q
Define ORF: Open Reading Frame
A
- DNA sequence produces RNA with start and stop
- Series of triplet codons specify amino acids to make polypeptide
14
Q
Explain Transcription
A
- 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
15
Q
Explain RNA Polymerase
A
- 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!!!
16
Q
Define Promoters
A
- 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)
17
Q
T/F: Promoters are always upstream to the + site
A
TRUE!!
18
Q
Pol 2 makes what type of RNA?
A
mRNA
19
Q
What happens during the Transcription start site
A
- DNA double helix is denatured: unwound to make template strand accessible for RNA polymerase
- Interaction of promoters and RNA polymerase regulates efficiency of transcription
20
Q
What are Consensus sequences?
A
DNA sequences homologous in different genes of same organism
21
Q
What are the 2 consensus sequences of E. coli promoters?
A
- TTGACA and TATAAT (Pribnow box)
- Positioned at −35 and −10 with respect to the transcription initiation site
- (-10) = 10 bases before the start site
22
Q
Explain Chain Elongation
A
- Ribosomes are added to RNA chain
- σ subunit dissociates from holoenzyme
- Elongation proceeds under direction of core enzyme
23
Q
In bacteria, there are 2 type of Terminations involving rho. Explain them
A
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.
24
Q
Explain Termination
A
- 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
25
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`
26
RNA Pol 1 Product AND Location
Product: rRNA
Location: Nucleolus
27
RNA Pol 2 Product and Location
Product: mRNA, snRNA
Location: Nucleoplasm
28
RNA Pol 3 Product and Location
Product: 5SrRNA and tRNA
Location: Nucleoplasm
29
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
30
What is the TATA Box?
- Core-promoter element
- Binds TATA-binding protein (TBP) of transcription factor TFIID: determines start transcription start site
31
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
32
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
33
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
34
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
35
Understand Posttranscriptional modifications: Splicing
- Introns are removed by splicing
- Exons are then joined together in mature mRNA
- Mature mRNA is smaller than initial RNA
36
Why do we even have introns?
Introns give diversity depending on how splicing takes place
Ex.) Hemoglobin and Myoglobin
37
Define Self-Splicing RNAs
Self-excision group I introns
occurs in bacteria, lower
eukaryotes, and higher
plants
38
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
39
What are the 2 forms of RNA editing?
Substitution editing and Insertion/deletion editing
40
Define Substitution editing
Identities of individual nucleotide bases are altered; prevalent in mitochondria and chloroplast RNA derived in plants
41
Define Insertion/Deletion editing
* Nucleotides are added/deleted from total number of bases
* Prevalent in mitochondrial and chloroplast RNAs
42
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
43
What are the only 2 amino acids encoded by a SINGLE codon?
Tryptophan and Methionine
