Module 1--Genes & Mutations Flashcards
What are the two levels of specificity that tRNA exhibit?
Aminoacyl-tRNA synthesise specificity (specify the correct amino acid to be added) and codon specificity (specify if the right tRNA is used during translation)
What are the interactions between codon and anticodon?
Hydrogen bonds
How are the abnormal bases in tRNAs created?
Post-transcriptional modification
What is the best-know abnormal base in tRNA?
Inosine
What bases does inosine forms hydrogen bonds with?
C, A and U, but not G
List the components of a cell-free protein synthesising system
- amino acids + tRNA
- ribosomes + ATP + GTP
- amino acids
- synthetic RNA
- one 14C amino acid
What are the alternative start codons do prokaryotes use?
GUG and UUG (only at start)
In Candida species, what codon encodes serine instead of leucine?
CUG
According to Wobble Rules, what bases does U in 1st position in anticodon binds to?
A or G
According to Wobble Rules, what bases does G in 1st position in anticodon binds to?
U or C
According to Wobble Rules, what bases does I in 1st position in anticodon binds to?
U, C or A
What is RNA polymerase reading?
RNA polymerase creates an RNA molecule complementary to the template strand
What is reading frame?
Refers to the position at which you start reading nucleic acid in 3 nucleotide codons
What is open reading frame (ORF)?
A region in any reading frame that begins with a start codon (ATG) and ends with a stop codon
Why mutation is inevitable?
DNA is not totally chemically stable:
- Spontaneous deamination of cytosine to uracil
- Spontaneous hydrolysis of purines
What is spontaneous mutation?
It occurs due to inherent metabolic errors or unknown agents in environment
What is induced mutation?
It results from exposure of organisms to mutagens
What is germinal mutation?
It occurs in germ-line cells and will be transmitted through the gametes to the progeny
What is somatic mutation?
It occurs in somatic cells; the mutant phenotype will occur only in that cell and its direct descendent
Does environmental stress cause specific mutations?
No, environmental stress selects for mutants that are best adapted to the environmental stress; mutation does not occur in response to specific needs
What is stationary-phase mutagenesis?
A process that increases spontaneous mutation rate in a cell, potentially creating a mutant with a selective advantage in a certain environment
When does stationary-phase mutagenesis occur?
It occurs when populations of bacteria of fungi stop growing
What is a forward mutation?
A mutation of a wild-type allele to a mutant allele
What is a reverse mutation?
A second mutation that restores to the original phenotype
What is a back mutation?
A kind of reverse mutation with a second mutation at the same site
What is suppressor mutation?
A kind of reverse mutation when a second mutation at a different location in the genome overcomes the deleterious effect of the first mutation
What is isoallele?
It has no effect on phenotype or small effects that can be recognised only by special techniques
What is null allele?
It results in no gene product or totally nonfunctional gene products
What is neutral mutation?
It has no effect on phenotype and produces isoalleles
What is recessive lethal mutation?
It is lethal in homozygous state
What is conditional lethal mutation?
It is lethal in restrictive condition and viable in permissive condition
What is auxotroph?
Mutant organism that is unable to synthesise an essential metabolite that is synthesised by prototrophs, and can grow only when it is supplied in the medium
What is temperature-sensitive mutant?
It grows at one temperature but not at another
What is suppressor-sensitive mutant?
It is viable only when a second genetic factor (a suppressor) is present
What are the major classes of mutation?
Substitution, inversion, insertion and deletion
What is silent mutation?
It does not change the gene product expressed by an organism
What is synonymous mutation?
A kind of point mutation that causes change in codon, but no amino acid change
What is non-synonymous, conservative substitution?
A kind of point mutation in which the new amino acid that has similar physical properties to the old one
What is non-synonymous, non-conservative substitution?
A kind of point mutation in which the new amino acid that has very different physical properties to the old one
Which amino acids are non-polar and aliphatic?
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine
Which amino acids are polar and uncharged?
Serine, Threonine, Cysteine, Asparagine, Glutamine
Which amino acids are aromatic?
Phenylalanine, Tyrosine, Tryptophan
Which amino acids are positively charged?
Lysine, Arginine, Histidine
Which amino acids are negatively charged?
Aspartate, Glutamate
What is missense mutation?
Amino acid substitution leads to protein being defective
What is nonsense mutation?
It creates a stop codon, prematurely ending the codon, often loss of function
How tautomeric shifts affect base pairing?
A:C base pair and G:T base pair
What are the types of substitution?
- Transitions: pyrimidine pyrimidine; purine purine
- Transversions: pyrimidine purine
What is the effect of nitrous acid?
Oxidative Deamination of bases
What mutagenesis is caused by ultraviolet radiation?
- Hydrolysis of cytosine may cause misfiring during replication
- Cross-linking of adjacent thymine forms thymine dimers, which block DNA replication and activate error-prone DNA repair mechanism
What can cause frameshift mutations?
Insertions or deletions in an ORF
What are the effects of ionising radiation?
It breaks chromosomes and can cause deletions, duplications, inversions, and translocations
What is the effect of hydroxylamine agent?
It hydroxylates the amino group of cytosine and leads to G:C –> A:T transitions
What is the effect of alkylating agent?
It donates alkyl groups to other molecules, causing transitions, transversions, frameshift, and chromosome aberrations
What are the two mechanisms of suppressor mutation occurs within the original codon?
- Reversion to original amino acid
- Change to a different amino acid but with similar property
What is intragenic suppressor mutation?
When a second mutation occurs within the same gene but in different codon
What is intergenic suppressor mutation?
When a second mutation occurs in a different gene
What is the mechanism of tRNA intergenic suppressor mutation?
First mutation in ORF is deleterious to bacterium; second (suppressor) mutation in anticodon region of a tRNA gene restores full ORF function
What is amber mutation?
Tyr codon is converted to stop codon, UAC or UAU –> UAG (stop)
What is ochre codon?
TAA
What is opal codon?
TGA
What is the Ames test?
It screen chemicals for mutagenicity with histidine auxotrophic mutants of Salmonella
How can thymine dimers be removed?
By photoreactivation, a light dependent repair, or by postreplication repair
What is the mechanism of photoreactivation?
Photolyase absorbs blue light for energy, cleaves thymine dimers restoring original state
What is the function of a DNA repair endonuclease or endonuclease-containing complex?
It recognises, binds to, and excises the damaged base or bases
What are the two kinds of excision repair?
- Base excision repair: remove abnormal or chemically modified bases
- Nucleotide excision repair: remove larger defects
What is the general mechanism of excision repair?
- DNA repair endonuclease or endonuclease containing complex recognises, binds to, and excises the damaged base or bases
- DNA polymerase fills in the gap
- DNA ligase seals the break left by DNA polymerase
What is the mechanism of mismatch repair?
- MutS recognises mismatches and binds to them to initiate the repair process
- MutH and MutL join the complex
- MutH cleaves the unmethylated strand at hemimethylated GATC sequences on either side of the mismatch
- Excision require DNA helices II and an exonuclease
- DNA polymerase III fills in the gap and DNA ligase seals the nick
What is the mechanism of post replication repair?
- DNA polymerase III restarts DNA synthesis past the dimer, leaving a gap in the nascent strand
- RecA binds to the single strand of DNA at the gap and mediates base pairing
- DNA polymerase fills the gap and DNA ligase seals the nick
When is SOS response activated in E. coli?
When DNA is heavily damaged by mutagenic agents
What is the mechanism of SOS response?
- DNA polymerase V replicates DNA in damaged regions
- LexA normally binds to and represses DNA regions that regulate transcription of SOS response genes
- When extensive DNA damage occurs, RecA binds to single-stranded regions of DNA in damaged regions
- This activates RecA, which stimulates LexA to inactivate itself, turning on SOS
What is the Holliday Model?
1) Pairing of homologous chromosomes
2) Formation of single-strand breaks
3) Strand displacement
4) Strand exchange
5) Formation of covalent single-strand bridge
6) 3-D structure (chi structure)
7) Equivalent 3-D structure
8) Resolution of single-strand bridge
9) 2-D view
10) Recombinant chromosomes
Garrod’s concept regarding the relationship between gene and metabolism can best be described as:
One gene - one metabolic block
George W. Beadle and Edward L. Tatum refined the concept of the gene to state which original idea?
One gene - one enzyme
What is the modern concept of the gene?
- Gene controls synthesis of one polypeptide chain or RNA molecule
- Nucleotide pair is the smallest unit that can be mutated; it cannot be subdivided by recombination
What are the purposes of complementation test or trans test?
- Provides an operational definition of the gene when used with recessive mutations
- Determines whether mutations are in the same gene or different gene
How is the complementation test constructed?
- Geneticists construct trans heterozygotes:
- If the trans heterozygote has a mutant phenotype, the two mutations are in the same gene
- If the trans heterozygote has a wild-type phenotype, the two mutations are in different genes
When the two mutations are on the same chromosome, the arrangement is called:
Coupling configuration and cis configuration
When the two mutations are on different chromosome, the arrangement is called:
Coupling configuration and trans configuration
What is complementation test?
Introduction of two recessive mutations into the same cell to determine whether they are alleles of the same gene
