Genome
Define 'gene expression.'
Process by which information contained in genes is decoded to produce proteins that determine the phenotypic traits of organisms
During which phase of mitosis does DNA replication take place?
S phase
True or false: by definition, mutations are always transmitted to offspring.
False. Germline mutations can certainly be transmitted, but somatic (or acquired) mutations rarely are.
Describe how strand slippage during DNA replication can cause insertion and deletion mutations.
When strand slippage replication errors are not corrected, they become insertion and deletion mutations.
In the former, the newly synthesized strand loops out such that it contains an extra nucleotide.
In the latter, the template strand loops out, such that one nucleotide is omitted in the new strand.
How are dideoxyribose-containing nucleotides exploited to analyze DNA sequences?
DNA synthesis is allowed to unfold in the presence of small amounts of fluorescently labeled nucleotides containing dideoxyribose (instead of the usual deoxyribose sugar).
Because dideoxyribose lacks the 3' OH group essential for attachment of nucleotides to the growing DNA strand, chain growth is stopped.
This results in DNA segments that can be separated by electrophoresis, their sequence read directly from the gel (from bottom to top).
What is the typical eukaryotic genome size?
100-1000 Mb
True or false: covalent bonds between DNA bases break during DNA replication to allow strand separation.
False. Strand separation occurs via the breaking of hydrogen bonds between DNA bases.
Define 'point mutation.'
Type of mutation in which one single nucleotide base is added, deleted or changed
Describe how corrected strand slippage replication errors can cause expanded trinucleotide repeats.
During replication of a trinucleotide repeat, the 3' end of the growing strand "breathes" (detaches from the template) and reanneals to the template at a point upstream from its original location.
Continued replication duplicates the region between the points of detachment and reannealing.
Mismatch repair of the shorter strand creates a duplex with a trinucleotide expansion.
True or false: genotyping detects small genetic differences, including single-nucleotide polymorphisms (SNPs), that leads to changes in phenotype.
True!
True or false: chloroplasts contain DNA.
True! (In addition to the nuclei and mitochondria of eukaryotes, of course)
True or false: in the semi-conservative Watson-Crick model of DNA replication, only one strand of DNA serves as a parent strand.
False. Both strands of the original DNA double helix serve as parent strands, allowing formation of two daughter strands, ultimately doubling the number of DNA helices.
True or false: all point mutations are clinically appreciable.
False. Point mutations come in various varieties, including: (1) silent mutations (not appreciable), (2) nonsense mutations (code premature stop), (3a) conservative missense mutations (nucleotide base substituted is similar to original) and (3b) non-conservative missense mutations (nucleotide base substituted is dissimilar, eg, in polarity, to original).
Give an example of a genetic disease associated with dynamic mutation (and the associated mutation).
1) fragile-X syndrome (dynamic mutation in the CGG repeat present in the FMR1 gene)
2) myotonic dystrophy (CTG)
3) kennedy disease (AGC)
4) friedreich ataxia (AAG)
5) spinocerebellar ataxia type 1 (AGC)
6) huntington disease (AGC)
Define 'polymorphism.'
Sequence variant found in a population; part of the natural variation of a population (usually >1% frequency)
Define 'C-value.'
Amount of DNA in the haploid genome of an organism
In what direction does DNA synthesis proceed?
5' to 3'
Give an example how a mutation outside the coding sequence may nonetheless affect gene interpretation.
1) promoter: increase/decrease transcription
2) regulatory region: inhibit regulation
3) 5'-UTR or 3'-UTR: affect translation or mRNA stability
4) splice recognition sequence: abnormal splicing of pre-mRNA into processed mRNA
How many CGG repeats in FMR1, Xq27, the gene underlying fragile X syndrome, are considered "pre-mutation" range.
55-200 repeats constitutes "pre-mutation."
5-44 = normal
45-54 = intermediate
55-200 = pre-mutation
>200 = pathological
What does the abbreviation RFLP present and how are RFLPs used to sequence DNA?
RFLP = Restriction Fragment Length Polymorphism
1) Restriction fragment preparation (DNA + restriction enzyme)
2) Electrophoresis
3) Blotting (Southern Blot)
4) Hybridization with radioactive probe
5) Autoradiography
Homologous DNA samples with differing locations of restriction enzyme sites are digested and blotted so that the resulting fragments (alleles) can be run on gels and compared by size.
Define 'C-value Paradox' and give a possible explanation of it.
Among eukaryotes, there is no consistent relationship between the C-value and the complexity of the organism.
This is because, in higher organisms, much of the DNA has functions other than coding for the amino acid sequence of proteins.
A trace amount of radioactively labeled dATP (phosphorous furthest from 5' carbon is radioactive) is added to a rapidly dividing population of E. coli.
Why, after 5 minutes, when the DNA is isolated and analyzed for presence of radioactivity, is none found in either small or large DNA fragments?
Because nucleotide triphosphate is cleaved to a monophosphate (with the two radioactively labeled phosphates supplying bonding energy) when the nucleotide is added to the growing sugar-phosphate backbone (held together by phosphodiester bonds)
Which of the following is an example of a somatic mutation?
A) mutation in an adult hepatocyte (liver cell)
B) mutation in an embryonic neuron
C) mutation in an oocyte
D) both A and B
D
Why is fragile X syndrome mostly seen in males?
Because its inheritance pattern is X-linked recessive, females with one mutated gene are protected by the corresponding wild type allele on their second X chromosome, while males, with just one X chromosome (and one Y), experience no such mitigation.
Compare 'minisatellites' and 'microsatellites.'
microsatellite = shorter than minisatellite; aka short tandem repeats (STRs), or simple sequence repeats (SSRs)
*VNTR can also refer to the broader category that includes BOTH size repeats (confusing!)